Get it wrong, and the consequences aren't small. Denied claims, underpayment, and even False Claims Act exposure are all on the table. Many practices struggle to keep direct billing, incident-to rules, and split/shared visits straight, and that confusion costs real money.
This guide breaks down CPT codes, reimbursement rules, incident-to billing, modifiers, and the mistakes that trigger audits.
Key Takeaways
- PAs can bill Medicare directly under their own NPI at 85% of the physician fee schedule
- Incident-to billing allows 100% reimbursement but demands strict compliance with Medicare's supervision rules
- Correct CPT codes and modifiers (like AS and FS) prevent denials and reduce audit risk
- Certified billing partners cut denial rates and protect revenue that practices would otherwise lose
Understanding How Physician Assistants Are Reimbursed
PAs are classified as non-physician practitioners (NPPs). Since January 1, 2022, CMS has allowed them to bill Medicare directly under their own NPI, under the CMS 2022 Physician Fee Schedule final rule.
Practices have two reimbursement paths:
- Direct billing: PA bills under their own NPI, paid at 85% of the physician fee schedule
- Incident-to billing: Supervising physician bills, paid at 100% of the fee schedule, but only when strict conditions are met
Commercial payers don't automatically follow Medicare's playbook. Some insurers mirror CMS rules closely; others don't allow incident-to billing at all. Always check the payer contract before assuming a Medicare rule applies.
Direct Billing Requirements
Before a PA can bill directly, a practice needs three things locked down:
- NPI enrollment - the PA must have their own National Provider Identifier
- Payer credentialing - separate from Medicare enrollment, and required individually for each commercial plan
- Documentation standards - notes must clearly support the service billed, independent of physician involvement
Skipping credentialing is one of the fastest ways to see a clean-looking claim bounce back unpaid.
Incident-to Billing Rules
Incident-to billing only works in outpatient or office settings — never in hospitals or emergency departments. Medicare requires:
- The physician performed the initial visit and established the treatment plan
- The patient is established, not new, and not presenting with a new problem
- The supervising physician is physically present in the office suite (not necessarily in the room)
Compliant example: A physician diagnoses a patient with hypertension and sets a treatment plan. The PA sees the same patient for a follow-up medication check while the physician works elsewhere in the office. That's billable incident-to.
Non-compliant example: That same patient shows up with a new complaint, say, chest pain. The PA evaluates it, but there's no established plan for this issue. This must be billed under the PA's own NPI at 85%, not incident-to.
CPT Codes and Modifiers for PA Billing
Here's something that surprises a lot of practice managers: PAs don't have their own set of procedure codes. They use the same CPT and E&M codes as physicians. The difference lies in who's billing and which modifiers apply.
The Modifiers That Actually Matter
- AS modifier: For assistant-at-surgery services by a PA only—not a generic “PA involved” flag. CMS pays roughly 13.6% of the physician fee
- FS modifier: Required on split/shared E&M visits in facility settings, regardless of which provider performed the substantive portion
Misusing AS on routine office visits is a common trigger for claim edits and repricing.
Quick reference for common PA scenarios:
- Assistant at surgery → append AS; expect the reduced assistant rate
- Split/shared facility E&M → append FS on the claim
- Routine office E&M under incident-to or direct billing → do not use AS
Specialty Nuances Matter
Modifier choice is only half the job. Specialty rules decide which CPT codes and documentation support the claim.
Behavioral health billing has its own requirements. Codes like 90832–90838 (psychotherapy) and 90791/90792 (psychiatric evaluations) need documentation that clearly ties the service to the credentialed provider.
Family medicine and internal medicine face a different challenge: matching MDM-based versus time-based documentation to the correct E&M level. Get leveling wrong, and you either leave money on the table or invite an audit.
Split/Shared Billing Between Physicians and PAs
Split/shared visits happen when a physician and a PA both contribute to the same patient encounter in a facility setting. That means a hospital or outpatient department — not a private office.
As of CY 2024, the billing decision hinges on the substantive portion rule:
- More than half of the total time spent on the visit, or
- A substantive part of the medical decision-making (MDM)
Whichever provider performed the substantive portion bills the claim under their own NPI, with the FS modifier attached.
CMS has redefined that standard more than once, so documentation habits that worked two years ago can fail an audit today:
| Period | Substantive Portion Standard |
|---|---|
| CY 2022 | Key component OR more than half of total time |
| CY 2023 | History, exam, MDM, or more than half of total time |
| CY 2024+ | More than half of total time OR substantive MDM |
Warning: Split/shared billing applies only in institutional facility settings, where incident-to billing is not permitted. Do not relabel an office visit as split/shared just because both a physician and a PA touched the chart.
Common PA Billing Mistakes and Compliance Risks
Most PA billing errors fall into a handful of predictable categories:
- Billing a new problem as incident-to when it doesn't qualify
- Using the physician's NPI without meeting supervision or initial-visit requirements
- Failing to enroll or credential the PA before submitting claims
- Applying the AS modifier to routine office visits instead of surgical assists
- Omitting FS on legitimate facility split/shared claims
These aren't just paperwork issues. They can trigger payer audits, refund demands, or False Claims Act exposure.
The Department of Justice resolved a case involving a New Jersey physician practice that billed services as physician-performed when nurse practitioners actually delivered them. The practice agreed to pay $106,255 to resolve the allegations.
That case involved NPs rather than PAs, and DOJ made no determination of liability—but it shows the billing-identity risk PA-staffed practices need to avoid.
Why Practices Rely on Specialized Billing Partners
PA billing complexity adds up fast, especially for practices juggling multiple specialties, provider types, and payer rules. Without dedicated coding expertise, revenue tends to leak through denied claims, misapplied modifiers, and missed incident-to opportunities.
Persistex Medical Billing works with independent practices across Massachusetts and New England on this kind of multi-provider billing complexity. That includes family medicine, internal medicine, primary care, pediatrics, and behavioral health clinics.
The team holds CPC and CPB certifications through AAPC. Coding covers MDM- and time-based E&M leveling for practices that run PA and physician documentation side by side.
Results speak to the approach:
- 98% clean claim rate across clients
- 35% reduction in coding-related denials
- 72% appeals success rate on denied claims
- 40% fewer denials at one 8-provider clinic, plus $85K higher monthly collections and A/R at 22 days
Persistex integrates with major EHR and practice management systems, including AdvancedMD, Kareo, athenahealth, DrChrono, and TherapyNotes, so PA claims move through existing workflows without disruption. Most practices are fully onboarded within 2-4 weeks.
Frequently Asked Questions
What CPT codes are used for billing physician assistant services?
PAs generally use the same E/M and procedure CPT codes as physicians since there's no separate PA-specific code set. Modifiers such as AS (assistant-at-surgery) or FS (split/shared visits) flag PA involvement where payers require it.
What are the Medicare billing guidelines for physician assistants?
PAs can bill directly under their own NPI at 85% of the physician fee schedule, or practices can bill incident-to at 100% when strict supervision and documentation requirements are met. The setting and treatment history determine which path applies.
What modifiers are used for billing physician assistant services?
The AS modifier applies specifically to assistant-at-surgery services performed by a PA. The FS modifier is required on split/shared E/M visits in facility settings to flag the billing arrangement.
Can physician assistants bill Medicare independently?
Yes. Since January 2022, PAs can bill Medicare directly under their own NPI for covered services, reimbursed at 85% of the physician fee schedule rate.
Is incident-to billing being phased out for PAs?
MedPAC has recommended eliminating incident-to billing for PAs and requiring direct billing instead, arguing it causes Medicare to undercount PA encounters. No final rule has changed this yet, but practices should watch for future CMS action.
How can practices reduce denials on PA-billed claims?
Verify documentation, NPI selection, and modifiers before every submission—most PA denials start there. A certified billing team that knows PA-specific payer rules can catch gaps early and cut repeat denials.
