MIPS Physical Therapy Billing & Eligibility

Read about billing through the Merit-Based Incentive Program System for physical therapists. Learn about MIPS eligibility at Healthie.

Over the past year, the pandemic has challenged healthcare providers to find secure and effective ways to continue to provide high-quality care to their patients. Many practitioners are beginning to implement a value-based approach to care, which means they are reimbursed based on their patients’ health outcomes, rather than by each service provided. Patients, therefore, see lower healthcare costs and providers improve patient satisfaction due to improved patient conditions.  

For physical and occupational therapists, the Center for Medicare Services has a number of value-based payment programs for their Medicare patients. Providers are reimbursed through incentive payments, determined by the quality of care given to their patients. Here, we’ve detailed the process of Medicare billing through the Merit-Based Incentive Program System (MIPS) for rehab therapists that are eligible to participate. 

What is the Merit-Based Incentive Program System?

Over the past few years, CMS has been making a push for value-based initiatives, meaning providers will be rewarded with incentive payments for the quality of care they provide Medicare patients. To begin implementing this goal, in 2015, the Medicare Access and CHIP Reauthorization Act was passed, replacing the Sustainable Growth Rate payment system with the more effective Quality Payment Program.  

The goal of the QPP was to incentivize practitioners to provide a higher quality of care for patients in order to be reimbursed at a higher rate, rather than rely on a high service volume to increase their income. The QPP is made up of two different paths that clinicians can follow in order to receive payment from CMS, depending on their specialty, practice size, and service volume. The two paths are: Merit-Based Incentive Program System (MIPS) and Advanced Alternative Payment Methods. 

The Merit-Based Incentive Payment System, therefore, is a program designed to implement quality-based care payments, by evaluating patient health outcomes and provider performance and adjusting reimbursement rates based on an overall score. 

Who is eligible for MIPS Physical Therapy Billing?

There are a number of eligibility criteria for physicians to participate in MIPS. These include:

  1. Having a Taxpayer Identification Number (TIN) and a National Provider Identification Number (NPI)
  2. Being one of the eligible clinician types, which includes physical and occupational therapists
  3. Exceeding the low-volume threshold for all three criteria, meaning the practitioner receives more than $90,000 a year in Medicare Part B payments, provides care for more than 200 Part-B enrolled Medicare beneficiaries, and bills more than 200 professional services.

How do you know if you are eligible as an individual or a group? This distinction is made based on provider TINs. If you are a provider with an individual NPI and TIN, then you are eligible as an individual. However, if you have multiple providers with individual NPIs that bill under a single TIN, then they are assessed as a group. 

CMS uses the MIPS determination period to evaluate individuals or groups of providers to determine whether they qualify for MIPS. This is a two year-period that is split into two one-year segments, from October 1-September 30, and the subsequent October 1-to September 30; for example, the current period would be October 1 2019 to September 30, 2020 and then October 1, 2020 to September 30, 2021. 

Voluntary Participation

If all three of these criteria are met, practitioners are required to participate in MIPS. There may be cases, however, in which providers are eligible, but not required. These include:

  1. Opt-In Participation: Individuals who exceed 1-2 of the low-volume threshold criteria and groups who exceed 1-3 of the criteria; these groups are still subject to the payment adjustment 
  2. Voluntary Participation: Those who do not exceed the low-volume threshold can report data without being subject to the payment adjustment

For individual providers looking to determine if they are eligible, CMS has provided an easy to use search tool that only requires your NPI number. Click here for a direct link to the CMS search tool. 

MIPS Scoring, Data Reporting, and Payment Adjustments


MIPS-participating providers report data and are scored in four categories:

  1. Promoting interoperability: includes patient engagement and the electronic exchange of health information, 25% of score
  2. Quality: includes the overall quality of care delivered, determined by CMS performance measures, 40% of score
  3. Improvement Activities: includes activities that assess how you improve your care processes, patient engagement, and access to care, 15% of score
  4. Cost: includes measuring the total cost of care over the year or the cost of a hospital stay based on your filed claims, 20% of score

Within each category, there are a number of small criteria that are assessed to make up the overall score. You can read detailed descriptions of each category’s requirements as described by CMS here

As a note, for 2021, physical and occupational therapists will only be scored in the Quality and Improvement Activities categories. 

MIPS Reporting

There are five different mechanisms by which practitioners can submit MIPS data at the end of each calendar year:

  1. Medicare Part B Claims: Only available to small practices (15 practitioners or less), quality data can be simply reported through your routine billing process
  2. Direct: Practitioners can use a third-party intermediary (such as EHRs and qualified clinical data registries) to submit data via an API or other electronic interaction
  3. CMS Web Interface: Only available to larger practices (25 practitioners or more), data can be submitted through a specified web platform created by CMS
  4. Log-in and attest: Practitioners can log in and manually attest to data submission
  5. Log-in and upload: Practitioners can log in and manually upload data in a CMS-approved format

Depending on the scoring category, practitioners may have to submit data via a different mechanism:


  • Individual: Medicare Part B Claims, Direct, Log-in and Upload
  • Group: Medicare Part B Claims (15 or less), CMS Web Interface (25 or more), Direct, Log-in and Upload

Improvement Activities 

  • Individual, Group, Third-Party Intermediaries: Direct, Log-in and Upload, Log-in and Attest

Promoting Interoperability

  • Individual, Group: Log-in and Upload, Log-in and Attest
  • Third-Party Intermediaries: Log-in and Upload, Log-in and Attest, Direct


  • There is no need to submit data; CMS will collect data from your claims. 

Payment Adjustments

At the end of each calendar year, practitioners will submit their relevant data to CMS and receive a MIPS score ranging anywhere from 0-100 before the start of the payment year. The payment year, however, occurs two years after data is submitted. For example, if you submit data for 2019, your payments for 2021 will be adjusted based on your 2019 MIPS score. In 2021, payment adjustments can occur +/-7%, and will grow to +/-9% for 2022 and beyond. 

Healthie for Physical Therapy Billing

With a range of carefully considered features and an intuitive interface, Healthie is proud to offer the best billing software solution for physical therapists. Healthie:

  • Uses an all-in-one system to integrate billing with scheduling, charting, reporting, client engagement, and more
  • Saves you time on administrative tasks by manually pre-filling Superbills, CMS 1500 forms, and invoices
  • Directly integrates with Office Ally to allow you to send, receive, and check on claims
  • Allows quick, safe, and secure payment through Stripe
  • Is fully HIPAA compliant 

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