Best Physical Therapy Software 2021

We'll help you find the best EMR and practice management software for your clinic, highlighting some top solutions developed specifically for the physical therapy industry.

WebPT: Best Web-Based Software

WebPT is a popular web-based HIPAA-compliant physical therapy EMR solution serving more than 64,000 users across 9,100+ clinics, most of which are private practices focused in outpatient therapy. The software is widely known in the industry for its exceptional documentation and scheduling capabilities. WebPT offers billing capabilities, but it also integrates seamlessly with many of the top billing solutions, in case you want to keep using your existing billing software. Since the software is 100% web-based, you have the flexibility to access the software and complete important tasks on the go. Read our in-depth WebPT review


  • Exceptionally strong documentation and scheduling capabilities.
  • 100% web-based, so you can access your clinic’s information on the fly.
  • With over 300 full time employees, the company is able to make weekly software updates, which means that you’ll get a product that’s constantly improving.


  • Month-to-month per-provider pricing with no annual contracts.
  • Free demo.
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WebPT is a favorite amongst physical therapists, with a 99% clinic retention rate.

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APTA Connect (by Cedaron Medical): Best For Hospitals

APTA Connect is an integrated specialty rehabilitation documentation, reporting, and scheduling solution developed in partnership with the APTA (American Physical Therapy Association). The software seamlessly integrates with any HL7-compliant software as well as most billing solutions, making it especially popular amongst hospitals that use multiple secondary EMR systems throughout the departments. In addition, Connect allows you to add your information to the APTA National Outcomes Database, which was developed by the APTA in order to help therapists understand the effectiveness of different treatments. Users find Connect to be highly customizable, making it an attractive option for hospitals dealing with a large number of specialty therapy / niche areas.


  • Developed in partnership with the APTA.
  • Outcomes tracking: participate in the APTA National Outcomes Database, and use the data to provide the best care for your patients.
  • Integrates with any HL7-compliant software as well as most billing solutions.


  • Varies based on number of FTE clinical users. Contact Cedaron to get a quote for your practice.
  • Free demo.
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Ideal for hospitals looking to participate in a national outcomes database.

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BestPT: PT-Specific Billing Software

BestPT (by Billing Dynamix) is a cloud-based practice management solution designed specifically for private physical therapy clinics. BestPT’s primary strengths are in its billing capabilities, where the software automatically checks each claim against more than 1.5M quality assurance rules to catch billing mistakes even before claims get sent out. The software is also fully integrated with other industry leaders in the physical therapy software space, such as WebPT and Cedaron Connect. This allows you to leverage BestPT’s billing expertise and customer support, while still enjoying the documentation and scheduling benefits provided by other industry-leading software providers.


  • Strong billing and reporting capabilities, with emphasis on communication and personalized support for all clients.
  • Over 1.5M billing Quality Assurance rules updated daily, so you will automatically be alerted when a claim has an error, even before it gets sent out.
  • Clients can either handle billing in-house, or outsource to one of BestPT’s expert billing teams.


  • $1495 startup fee, with no recurring monthly fees.
  • Additional fees based on how much you bill, and whether you outsource your billing or do it in-house. In-house billing costs $.79 per claim, and outsourcing to BestPT's team of expert billers costs 6-7% of each dollar that's reimbursed, which is about average for the industry.
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Ideal for established medium-sized physical therapy practices looking to streamline their billing process.

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TheraOffice: Physical Therapy Software with Powerful Reporting Capabilities

Founded by an experienced physical therapist, TheraOffice's leadership team understands the nuances and complexities of generating accurate, detailed documentation. The software is designed to help physical therapists save time, improve their workflow processes, and spend more time on what really matters: delivering excellent quality care to their patients. The software includes many helpful features like tasks, alerts, and documentation templates, but all of these features are fully customizable, meaning that they can be modified to suit your preferences and needs. The software also includes an extraordinary number of built-in reports (more than 175), but you can even work with the TheraOffice team to create additional custom reports as needed.


  • More than 175 reports in 17 categories to help you optimize and improve your practice's workflow and finances.
  • Customizable templates help automate more accurate, efficient documentation processes.
  • Regular software updates ensure that the product stays up to date with the latest industry changes, e.g. code updates.


  • Contact TheraOffice for a quote.
  • Free demo.

Ideal for practices that want to optimize their workflow and analyze reports to make data-driven decisions.

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Practice Fusion: Most Popular Free EHR

Practice Fusion is a free web-based EHR that is widely used across the medical industry, especially by smaller, cost-conscious medical practices. Though the software isn't designed specifically for physical therapists, it's still a worthy option to consider for PT clinics, as it has a lot of the necessary functionality, as well as many PT-specific charting templates. The software is endorsed by Dr. Oz, and has gained recognition as one of the premier free EHR system. Though the software is free, Practice Fusion can be used to perform various tasks like charting, scheduling, billing, and documentation, and many users report that its functionality is comparable to some more expensive EHR systems. Since the system is optimized for touchscreens, you can use the software on the go with your iPad or tablet, or desktop if you prefer.


  • Used by over 112,000 medical professionals.
  • Customizable templates make for fast documentation.
  • Includes patient portal, and online appointment booking.


  • Free (paid for by ads.)
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Ideal for smaller, cost-conscious medical practices looking for a complete EHR system.

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Office Ally: Free Clearinghouse & Affordable EHR

Office Ally is well-known across the medical industry, and is used by over 330,000 medical providers. Though Office Ally is known best for its free clearinghouse, Office Ally offers a suite of products that can be used for end-to-end management of your medical practice. In particular, Office Ally offers a low-cost comprehensive EHR, a free practice management system, and a free patient portal. Though not designed specifically for physical therapists, many cost-conscious rehab clinics use Office Ally.


  • Free clearinghouse enables users to submit electronic claims to over 5,000 payers.
  • Free practice management software, and low-cost EHR with customizable progress notes.


  • Free clearinghouse & practice management software.
  • EHR: $29.95 per month/provider.
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Ideal for practices looking for a free clearinghouse, and a budget friendly EHR that gets the job done.

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Kareo: Most Popular Billing Software

With a client base of over 35,000 providers, Kareo is one of the most trusted software vendors in the industry. Kareo offers various cloud-based software modules that can be purchased individually. Though the software isn't designed specifically for physical therapy businesses, PTs can use all of these modules as an end to end practice management and EMR solution. However, since Kareo is best known for its billing capabilities, many physical therapy clinics opt to use Kareo's billing module in combination with another EMR that integrates with Kareo. You can also opt to completely outsource your billing to Kareo's team of expert billers, for an additional fee.


  • Submit more accurate claims electronically, with automatic claims scrubbing.
  • Intuitive dashboard makes it easy to identify any claims that have been rejected or need follow-up.
  • Large client base, used by over 35,000 providers.


  • Billing module is $150/month per provider for unlimited claims. Additional charges for other modules (EMR, Marketing, etc.)
  • Contact Kareo to receive a quote for RCM services.
  • No setup fee.
BestPT Logo

Kareo is a leader in the medical billing software industry.

Other Top Physical Therapy Software Options

Clinicient is an EMR/billing solution that is focused on helping physical therapy practices generate more accurate claims and get paid more quickly.
Raintree offers a rehab-specific practice management system & EMR, designed for private rehab practices.
AdvancedMD provides a popular billing system, as well as EHR, designed for independent medical practices.
BMS Practice Solutions' web-based physical therapy practice management software is most known for its RevFlow reporting software, which helps therapists understand the analytics of their practice so that they can make smarter business decisions. BMS was acquired by WebPT in February 2018.

Key Questions
to Consider

  • Should you buy software designed specifically for physical therapists?

    There are many large, reputable players (e.g eClinicalWorks, Epic Systems, athenahealth) who offer general EMR and practice management software for the medical industry. However, they can be much more expensive, and may include many features that aren't relevant to physical therapists. If your practice covers multiple specialities in addition to phyiscal therapy, then it can make sense to consider one of the general EMR or practice management solutions. Otherwise, we suggest selecting a vendor who focuses on developing software specifically for the physical therapy industry, or one of the free EHR systems, such as Practice Fusion.

  • Does the software integrate with your other applications?

    If you're choosing an all-in-one solution that covers both EMR and practice management, then you're all set. But if you have a preferred billing software, for example, and are looking to select a more appropriate EMR for your business, you'll want to make sure that you select an option that will integrate with your billing software. Otherwise, you'll be forced to enter your data into both systems, which can be cumbersome and error-prone. Even if the solutions integrate with each other, some integrations require more effort on your part than others, so it's worth asking the software vendor about the details of the integration, so that you can understand exactly what needs to be done.

  • Will you have access to your data after switching providers?

    If you ultimately decide to leave a software vendor, it’s important to understand what will happen to your data after you transition. You want to make sure that you’ll have access to your data after you switch, and that it’ll be accessible in a format that’s easy to use or port over to your next software application. Many vendors (including some of the most popular ones) will either charge you for the data, or give it back to you in an encrypted or proprietary format that is pretty much unusable, unless you pay them to help you convert it. Therefore, we encourage you to ask your software vendor what will happen to your data in the event that you end your relationship with them.

  • Does the software support your operating system?

    Some solutions are only compatible with Windows PCs, which means that if you’re a Mac user, you'll have to look elsewhere. Ideally, software should be web-based, which means that it will be compatible with any operating system.

Important Product Features to Look For

  • Scheduling

    The scheduler should be intuitive, and integrated with the rest of the software (billing, patient records, etc.) It's nice to be able to color-code the schedule for different therapists or specialties. You also want to be able to schedule automatic appointment reminders in order to reduce no-shows, as well as schedule recurring appointments.

  • Billing

    You want to be able to submit claims electronically, and have the billing module be integrated with the documentation module, so that you won't have to enter the same data in multiple places. Some companies also enable you to outsource your billing completely, and will handle all claims rejections and follow-ups for you, at an additional charge (typically 6-7% of each dollar that's reimbursed.)

  • Documentation

    The software should help you write compliant documentation quickly, and alert you when there's important missing information. It's also important that the software makes it easy to select the appropriate ICD-10 codes, and enables you to bookmark frequently used codes.

  • Reporting

    Most software providers include standardized reports to help you analyze your business. You may also want to look for software that enables you to create custom reports.

  • Outcomes Tracking

    Outcomes tracking can be a useful tool in benchmarking your practice, and in making sure that your patients are receiving the best care possible. By participating in an outcomes tracking database, you'll have access to important data that will help you make the best data-driven decisions possible.

  • Supported Integrations

    If you're currently using software for a certain aspect of your business but are looking for additional software to supplement it, you'll want to make sure that the various programs are capable of integrating with each other. Otherwise, managing multiple programs can introduce additional problems.