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6 BEST Healthcare Credit Card Processing Companies in 2023

Dawn Prevete Dawn PreveteFinance Specialist October 18, 2023
October 18, 2023
Finding the right credit card processor is challenging for any business, but if you’re in the healthcare sector, there’s even more to consider.

That’s because not every processor offers HIPAA-compliant software or can integrate with software medical offices commonly use. And even those that do may not offer pricing models well-suited to your business. Just because one type of merchant account works for a physiotherapy clinic doesn’t mean it’ll work for a pharmacy.

That’s not to say you’re out on your own. I’ve researched dozens of credit card processing companies, and I’ve found some fantastic options that come with HIPAA-compliant software, excellent rates, and even free hardware. Leaders Merchant Services (LMS) is my top choice for its low rates and free POS hardware that comes with HIPAA-compliant payment tools. Plus, it offers tons of built-in security features to keep your data safe.

Let’s take a look at the best healthcare payment processing for medical offices available today.

Short on Time? These Are the Best Healthcare Credit Card Processors For Medical Offices in 2023

  1. Leaders Merchant Services – Negotiable pricing model for healthcare practices backed by a money-saving guarantee.
  2. PAYARC – Seamless integration with HIPAA-compliant payment and business management software.
  3. Stax – Powerful HIPAA-compliant business and payment management software for high-volume practices.

See 3 More Great Options | Comparison Table

What We Look For in the Best Healthcare Credit Card Processing For Medical Offices

There’s no one-size-fits-all approach to healthcare payment processing, but there are features that every medical office needs from its credit card processor.
  • HIPAA-compliant software. Software that’s used to access or store patient information needs to be HIPAA-compliant. Every payment processor on this list has its own software or can integrate with HIPAA-compliant software tools, making it easier to manage your administrative tasks.
  • E-commerce integrations. Whether you take appointment bookings online or allow patients to order and pay for their medication on your website, you’ll need e-commerce integrations to handle those transactions.
  • Chargeback and fraud protection. Chargebacks and so-called “friendly fraud” can present a significant threat to healthcare businesses, particularly when insurance companies don’t cover as many costs as the patient expects. Good healthcare merchant accounts come with built-in protection against fraudulent chargebacks and aid in disputing them if they arise.
  • Invoicing and payment plans. Depending on your practice, you may have patients that need to spread out the full cost of their bill or need extra time to pay your invoice. A good payment processor should give you a variety of payment plans so that your patients can pay for their treatment in whatever way suits them best.

A Note on HIPAA Compliance

Credit card processing itself is not considered a HIPAA-covered activity because you’re not storing any health-related information in your merchant account. If you’re only using a payment processor for this purpose, then it doesn’t need to have a BAA or be HIPAA-compliant.

However, any software you use – whether that’s built into your merchant account or offered as a third-party integration – needs to be HIPAA-compliant if it has access to personal health information (PHI). This includes the tools you use to manage invoices, bookings, health records, or any other aspect of your practice.

1. Leaders Merchant Services: Negotiate a Good Deal

Leaders Merchant Services (LMS) promises to meet or beat your current processing rates. It’s so confident that it can at least meet your current rates, it’ll give you a $200 AMEX gift card if it can’t. So, if you’ve been with your current credit card processor for at least two months, get in touch with an LMS sales agent – there’s a good chance that this credit card processor can offer you lower rates.

On top of some of the lowest per-transaction rates I’ve seen in an interchange-plus pricing model, you can also get free POS hardware if you’re willing to sign a long-term contract. You may also be able to negotiate multiple free terminals depending on your contract length and business needs. This goes to show the lengths LMS is prepared to go to provide the best solution possible for your specific healthcare business.

While LMS itself isn’t HIPAA-compliant, it is a certified Clover reseller, and Clover’s POS software is HIPAA-compliant. It even comes with additional management tools like invoicing, staff scheduling, and CRM software.

Features and Benefits

  • Merchant cash advances. LMS offers merchant cash advances to all its customers. If you’re unable to qualify for traditional financing, you’ll still be able to secure funding for your business through LMS.
  • 96% approval rate. If you’ve struggled to find a credit card processor for your healthcare business in the past, give LMS a try. In some cases, you’ll know whether you’ve been approved on the same day, and you’ll be able to start taking payments in a few days.
  • Add-on services. You can also negotiate additional services like loyalty programs and subscription payments, both of which can be extremely helpful for medical offices and specialized services.
  • 24/7 phone support. This is ideal for healthcare practices that take after-hours emergencies. No matter what issue you’re having, you can count on LMS support for help.
Read more about negotiating your rates in our Leaders Merchant Services review.

HIPAA compliant? No, but integrates with software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (Authorize.net)
Other security features
  • PCI-compliant
  • Tokenization, end-to-end encryption
  • PCI compliance support for merchants
Transaction fees on cheapest plan ~2% + 0¢
Monthly fee on cheapest plan $9.00

2. PAYARC: Tailored Plans With HIPAA-Compliant Software Integration

PAYARC prides itself on tailoring its fees and features based on its client’s processing needs. Its client-centered approach is well-suited to the healthcare industry, regardless of whether you run an independent practice or a large hospital chain.

Healthcare practices can choose either an interchange plus or flat rate plan, though the interchange-plus plans are more appropriate for high-volume medical businesses.

Every plan includes an integration with Rectangle Health, which ensures your practice is both HIPAA and OSHA compliant. You’ll also get extensive management, reporting, and patient communication and collaboration tools.

In addition to meeting the highest level of PCI compliance for business-to-consumer (B2C) processing, PAYARC also meets stringent PCI standards for business-to-business (B2B) and business-to-government (B2G) payment processing. Whether you’re a healthcare, medical, dental, or specialty practice, PAYARC will give you the tools to manage client billing and payments securely.

Features and Benefits

  • Low-cost processing for non-profits. PAYARC offers special reduced rates for non-profit healthcare providers, including community centers, nursing homes, clinics, and hospitals. It even offers at-cost payment processing to qualified 501c providers.
  • Patient payment plans. Rectangle Health’s financing solution lets you focus on delivering  necessary care to your patients with no risk to your practice’s bottom line. Patients can choose from multiple fully funded plan options, which make it easier for them to manage bills. The approval rate is nearly 100%.
  • Reporting and analytics. Both PAYARC and Rectangle Health offer robust reporting capabilities, allowing healthcare practices to access detailed financial and operational reports. Insights into your practice’s revenue trends, payment collections, and other key metrics can help you make informed business decisions.
  • Communication tools. Features like automated appointment reminders, online scheduling, and secure messaging enhance patient engagement and satisfaction.
Read more about HIPAA-compliant software in our PAYARC review.

HIPAA compliant? (with Rectangle Health integration)
Fraud and chargeback support Transaction filters, transaction holds, AVS/CVV matching
Other security features
  • PCI compliant & OSHA compliant (with Rectangle Health)
  • Tokenization, end-to-end encryption, EMV & NFC capable
  • Chargeback mitigation plan
Transaction fees on cheapest plan 0% + 15¢ (in-person & online)
Monthly fee on cheapest plan $69.00

Offering both 0% markup on interchange fees and a full suite of HIPAA-compliant software for a single monthly fee, Stax is one of the best healthcare payment processors for high-volume medical offices. If you already use various software tools to manage your healthcare business, Stax can save you a significant amount on software fees alone. Overall, healthcare businesses can save up to 40% on their payment processing with Stax.

Every Stax plan gets you access to Stax Pay, which comes with financial analytics and reporting, a virtual terminal, and even an online customer review management dashboard. The Pro plan unlocks Stax’s powerful invoicing software, which you can use to set up branded invoices with embedded payment links.

Most importantly, Stax’s built-in security ensures your patients’ PHI remains secure. Stax is a PCI Level 1 credit card processor, which is the highest level of PCI compliance available. This means it needs to complete third-party security audits every year, have its network scanned quarterly, and employ an internal compliance team. It also uses end-to-end encryption and tokenization to keep your data secure.

Features and Benefits

  • Accept FSA/HSA. Stax merchant accounts can accept payments directly from a patient’s FSA or HSA account, making it even easier for your patients to pay you on time.
  • Payment plans. You can set up payment plans on Stax’s Ultimate plan, which is ideal for healthcare practices that regularly charge for expensive procedures that clients may not be able to pay for in one go. You can also store payment methods for patients with recurring billing.
  • Fraud protection. Stax uses address verification (AVS) to detect potentially fraudulent transactions. If AVS can’t completely verify a customer’s identity, Stax will put a hold on their account until you receive additional verification.
  • 24/7 support. Stax offers 24/7 phone support and a comprehensive knowledge base. If you run a busy healthcare practice and can only contact support outside of business hours, it’s good to know someone’s always available at Stax to help you out.
Read more about this processor’s software suite in our expert Stax review.

HIPAA compliant?
Fraud and chargeback support
  • Customer account holds
  • Chargeback support phone line
  • Transaction filters, transaction holds, AVS (Authorize.net)
Other security features
  • PCI Level 1 compliant
  • PCI compliance support for merchants
  • Tokenization, end-to-end encryption
Transaction fees on cheapest plan 0% + 10¢ (in-person)
Monthly fee on cheapest plan $99.00

If you’re looking for a payment processor built for the healthcare industry, you may want to consider Chase Payment Solutions. It offers a number of industry-specific payment tools, including the proprietary HIPAA-compliant InstaMed software.

InstaMed’s suite of business management and patient engagement solutions help improve efficiency and allow you and your staff to focus on patient care. Like Chase Payment Solutions InstaMed meets the highest PCI standards and offers robust security measures like tokenization and end-to-end encryption to keep patient and payment data safe.

If you’re a small- to mid-sized practice, Chase’s simple, flat rate pricing with no monthly or hidden fees makes it easier to predict costs and budget appropriately. Another perk is next-day and optional same-day payouts with a Chase Business account.

Besides your per-transaction fees, all you’ll have to pay is a low monthly fee for the InstaMed software.

Features and Benefits

  • Seamless HIPAA software integration. InstaMed smoothly integrates with existing healthcare IT systems and electronic health record (EHR) software. With all patient payment data and financial information on a single, user-friendly platform, you and your staff can spend more time on patient care and less time on administrative tasks.
  • Optimized patient portal. Patients can view their bills, make payments, set up payment plans, and store payment methods for future use. This can improve overall patient satisfaction and increase the chance of timely payments.
  • Automated payment processing. InstaMed offers automated payment posting to your practice’s management system, reducing manual data entry and minimizing errors. With auto-reconciliation of accounts, you can streamline revenue cycles and improve your practice’s financial performance.
  • Useful mobile app. With the Chase app you can accept payments, create and send payment links, and manage your account from your smartphone. It’s available for Android and iOS.
See our expert Chase Payment Solutions review for more.

HIPAA compliant?  (with InstaMed)
Fraud and chargeback support Customer account holds, transaction filters, transaction holds, AVS (Authorize.net and Orbital virtual terminal)
Other security features
  • PCI Level 1 compliant
  • Zero liability protection
  • Regular security audits
  • Tokenization, end-to-end encryption
Transaction fees on cheapest plan 2.6% + 10¢
Monthly fee on cheapest plan N/A

If you’re on a budget but still need modern POS hardware, then you should consider Flagship Merchant Services. As with LMS, you’ll be able to negotiate the best pricing model, rates, and software for your business – and you’re covered by the same meet-or-beat guarantee. This, however, is where the similarities end.

Flagship offers free Clover Mini devices, provided you meet certain requirements not disclosed on the website. Obtaining one for free can save you a significant amount of money if your healthcare practice requires modern, smart POS devices. Just be aware that you’ll have to pay an extra cost to use Clover’s HIPAA-compliant software.

Features and Benefits

  • Same-day funding. While this comes at an extra cost, it’s ideal for meical offices that need a consistent cash flow to stay afloat.
  • Business financing. Flagship offers cash advances of up to $150,000 for all merchant accounts. You can repay the loan through a small commission on future sales.
  • Quick setup. Unlike other credit card processors, Flagship’s onboarding process is pretty fast. Once you’ve been accepted, you can start processing payments on the next business day.
  • iAccess business portal. This software suite is HIPAA-compliant and allows you to see sales summaries, generate financial reports, and even analyze how well your business is doing against the competition.
Read our Flagship Merchant Services review to see more great features.

HIPAA compliant? No, but integrates with software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (Authorize.net)
Other security features
  • PCI, GDPR, & CCPA compliant
  • Tokenization, end-to-end encryption
  • Regular merchant account security scans
Transaction fees on cheapest plan 1.58% + 19¢ (in person)
Monthly fee on cheapest plan $7.95

6. PaymentCloud: HIPAA-Compliant Processing for High-Risk Healthcare Firms

If you offer patient services like telemedicine, credit card processors might flag your practice as high-risk. That’s where PaymentCloud comes in. It supports both low- and high-risk health care providers with fairly priced interchange-plus and flat-rate plans.

In addition to HIPAA-compliant payment processing, PaymentCloud ensures the security of  your patients’ PHI (Protected Health Information) with a suite of robust security tools. All health and billing information is processed using end-to-end encryption and stored using tokenization, making PaymentCloud a trustworthy processor for any healthcare practice.

PaymentCloud is known for exceptional customer support and a hands-on approach to resolving chargeback issues – which it claims it can help you win 70% of the time. If your healthcare practice is mid- to high-risk, PaymentCloud is an excellent option.

Features and Benefits

  • Business management tools. PaymentCloud offers a suite of business management tools to streamline operations and automate routine tasks, from scheduling to inventory management and billing. This can help you increase your practice’s efficiency and allows you to focus on patient care.
  • Fraud and chargeback protection. PaymentCloud employs advanced fraud detection algorithms to identify and prevent suspicious activities in real time. By combining machine learning and rules-based approaches, PaymentCloud minimizes chargebacks and defends your practice from fraudulent transactions.
  • Flexible online payments. Easy-to-integrate payment gateways support credit card, e-checks, and mobile payments. PaymentCloud also offers a smooth and fast checkout experience, which can enhance patient satisfaction and help promote timely payments.
  • Financing options. For business credit lines to equipment funding, PaymentCloud offers a quick and simple answer for medical, dental, and other healthcare practices that require a cash boost. The funds can be accessible in just 24 hours.
Want to learn more about PaymentCloud? See our full review.

HIPAA compliant?
Fraud and chargeback support Alerts, transaction filters, transaction holds, AVS
Other security features
  • PCI-compliant
  • Tokenization, end-to-end encryption, IP tracking, automatic fraud alerts, payment holds
  • Multiple PCI-compliant payment gateways including Authorize.net, USAePay, and Cybersource
Transaction fees on cheapest plan Around 2.1% + 15¢
Monthly fee on cheapest plan $14.00

Which Is the Best Healthcare Credit Card Processing Company for Your Clinic?

It’s not always easy to find payment processors that offer affordable rates, HIPAA-compliant software, and great customer service. While there’s no one-size-fits-all solution, these are my top recommendations that will suit most healthcare businesses.

Overall, my top pick is Leaders Merchant Services. With some of the lowest rates in the industry and a fantastic meet-or-beat guarantee, you’ll be able to negotiate the best possible rates for your healthcare business. Plus, every LMS merchant account comes with Clover’s built-in HIPAA-compliant business and payment management tools.

If you’re looking for custom plans PAYARC lets you tailor your plan to your practice’s needs. Seamless integration with Rectangle Health offers advanced payment and management tools that can help increase efficiency and patient satisfaction.

Finally, if you run a bustling healthcare practice, I recommend Stax. Not only does Stax offer advanced HIPAA-compliant software for a single monthly fee, but it also doesn’t charge a markup on interchange fees – which can save you a lot of money if you process a high volume of transactions every month.

Here’s how the best healthcare credit card processing providers compare.

Best Feature Best For Monthly fee on cheapest plan Transaction fees on cheapest plan
Leaders Merchant Services Pricing models that are open to negotiation Healthcare businesses looking to secure processing rates $9.00 ~2% + 0¢
PAYARC Tailored plans and seamless integration with HIPAA/OSHA-compliant software Healthcare practices that need a custom plan and advanced HIPAA-compliant tools $69.00 0% + 15¢ (in-person & online)
Stax HIPAA-compliant business and payment management software Modern healthcare businesses that need a powerful software suite $99.00 0% + 10¢ (in-person)
Chase Payment Solutions Per-transaction fees only and health-care specific payment tools Lower volume practices that can benefit from flat rate pricing N/A 2.6% + 10¢
Flagship Merchant Services Free Clover Mini devices for qualifying merchant accounts Healthcare businesses that need modern POS hardware for their clinic $7.95 1.58% + 19¢ (in person)
PaymentCloud HIPAA-compliant processing for higher risk healthcare providers Healthcare businesses considered to be high-risk by most processors $14.00 Around 2.1% + 15¢


Which payment platforms offer are HIPAA-compliant processing?

Both Leaders Merchant Services and PAYARC offer exceptional HIPAA-compliant payment processing solutions. You can still use a non-HIPAA-compliant payment processor to accept credit cards within your clinic as this is classed as an exempt activity. If you need to use payments software like e-commerce platforms, shopping carts, or scheduling software, then you’ll need to check that it offers a Business Associate Agreement (BAA) for healthcare businesses.

What payment platforms are HIPAA-compliant?

There are a lot of HIPAA-compliant payment platforms on the market. For higher-riskvolume healthcare businesses, I recommend PaymentCloudStax. This payment processor offers a secure payment gateways, CRM, analytics software, and marketing integrations. You may also want to take a look at Leaders Merchant Services, which has some of the lowest rates on the market and plenty of modern payment tools to support your business.

Why is PayPal not HIPAA-compliant?

PayPal isn’t HIPAA-compliant as it doesn’t offer a BAA (Business Associate Agreement) to healthcare providers. On top of that, PayPal collects user data and sells it to advertisers, so there’s no guarantee that it would protect Public Health Information (PHI). If you need a HIPAA-compliant payment solution that offers great software, no contracts, and competitive pricing for small businesses, it’s worth considering Chase Payment Solutions.

What is the most common violation of HIPAA?

The most common HIPAA violation is the failure to secure and encrypt PHI. When it comes to payment processing, you can prevent this by using a processor that provides HIPAA-compliant software. You should also train staff that collect payments in data security. This means ensuring that there’s a designated secluded area to accept over-the-phone payments and immediately shredding documents containing PHI after use.

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