Behavioral Health Billing Services for PHP, IOP, Inpatient and Substance Use Programs

The Program Codes We Bill Most

Modifiers That Matter

Payer Rules to Know

Top Denials in Behavioral Health Billing Services for PHP, IOP, Inpatient and Substance Use Programs

What Is Behavioral Health Program Billing, and How Does It Differ from Therapy Billing?

Program billing is facility billing: the claim describes a day, a week or a stay in a program, and it goes on the UB-04 rather than the CMS-1500. Individual therapist and psychiatrist claims, with codes such as 90837 and 90791, are covered on our mental health billing page and are not repeated here.

How Are Partial Hospitalization and Intensive Outpatient Claims Built Under Medicare?

Hospitals and critical access hospitals report condition code 41 on a PHP claim and condition code 92 on an IOP claim, in form locators 18 to 28, and every covered service gets its own revenue code line (Claims Processing Manual, Chapter 4, sections 260.1 and 261.1). Medicare began paying for IOP on January 1, 2024, under the CY 2024 hospital outpatient final rule (88 FR 81540, published November 22, 2023).

The patient must fit the program. Under 42 CFR 410.43, PHP is for patients who need at least 20 hours of therapeutic services a week in the plan of care. Under 42 CFR 410.44, IOP is for patients who need at least 9 hours a week. Both require a mental health or substance use disorder diagnosis and a patient who does not need 24-hour care.

A physician must certify the stay and sign a written plan of care (42 CFR 424.24(d) and (e)). PHP is recertified as of the 18th day and then at least every 30 days. IOP is recertified at least every 60 days.

Hospitals other than critical access hospitals must report a HCPCS code on each revenue line; the contractor checks that a valid code is present, not that it matches the revenue code.

Report units for each HCPCS code. For codes with no time in the descriptor, the manual says hospitals do not bill sessions under 45 minutes. Each service repeats on its own line with its own date in form locator 45, and the record must show the beginning and ending time.

From CY 2024 the manual describes four PHP payment groups: APCs 5853 and 5854 for community mental health centers and 5863 and 5864 for hospital-based programs, split at three or fewer services a day versus four or more. See OPPS and APC rules and APCs.

Which Clinicians Bill Separately from the PHP or IOP, and Which Are Bundled?

Physicians, physician assistants, nurse practitioners, clinical nurse specialists and clinical psychologists bill the Medicare Part B contractor separately for their services to PHP and IOP patients. Everyone else is bundled into the facility claim (Chapter 4, sections 260.1 and 261.2; 42 CFR 410.43(b) and 410.44(b)).

Clinical social workers, marriage and family therapists, mental health counselors and occupational therapists are bundled. The hospital bills their time as program services and is paid on the facility claim (Chapter 4, section 270).

The same psychiatrist visit can appear on a UB-04 and a CMS-1500, and one will deny if both bill it. We reconcile professional charges against facility revenue lines before release.

How Do You Bill an Inpatient Psychiatric Stay?

An inpatient psychiatric facility (IPF) bills Medicare on type of bill 11X, one admit-through-discharge claim, and is paid a per diem under the IPF prospective payment system (42 CFR 412, subpart N). Chapter 3, section 190 of the Claims Processing Manual covers psychiatric hospitals and distinct-part psychiatric units.

The principal diagnosis drives the adjustment. For discharges on or after October 1, 2024, the manual says the system adjusts for 19 designated MS-DRGs, and a claim whose principal diagnosis does not group to one still receives the base per diem and the other adjustments. Physician visits during the stay bill separately; see hospitalist billing for hospital visit rules.

• Electroconvulsive therapy: report the number of treatments as service units on revenue code 0901, with an ICD-10-PCS code (GZB0ZZZ, GZB2ZZZ or GZB4ZZZ) and the date of the last treatment.
• Long stays: IPFs may interim bill in 60-day intervals, and late-charge claims are not allowed, so an adjustment must replace the whole claim.
• Lifetime limit: 42 CFR 409.62 sets 190 days of inpatient psychiatric hospital care per beneficiary, so eligibility checks should look at days already used.

How Do Opioid Treatment Program Bundles G2067 to G2080 Work?

An opioid treatment program bills one weekly bundle code per 7 contiguous days, chosen by the medication given, plus add-on codes for extra services. Only a Medicare-enrolled OTP may bill them, and OTPs may not bill other fee schedule codes for these services (Chapter 39, section 30.6).

The October 2026 HCPCS file shows G2070 to G2072 (buprenorphine implant bundles) with a termination date of December 31, 2024, and Chapter 39 omits them. Review any charge master that still carries them.

• Every claim needs an opioid use disorder diagnosis in the ICD-10-CM F11 range, on the bundle and each add-on (section 60).
• Professional claims use place of service 58, and the prescriber's NPI goes in box 17 of the CMS-1500 (sections 40.1 and 40.3).
• A second bundle inside 7 days needs modifier 59 and a documented reason, such as aligning a new patient to the weekly cycle or a holiday week.
• Counseling, intake and periodic assessments by audio-only telephone take modifier 93; audio-video takes 95.

Institutional OTP claims use bill type 013X, 085X or 087x, condition code 89 and revenue codes from the manual's list, including 0944 (drug rehabilitation) and 0953 (chemical dependency). Only the facility or the practitioner may bill, not both (section 50.1).

How Do You Bill SBIRT and Other Substance Use Services Outside an OTP?

SBIRT is screening, brief intervention and referral to treatment. Medicare identifies it with G0396 (15 to 30 minutes) and G0397 (more than 30 minutes) for a structured alcohol or drug assessment with brief intervention, and G2011 for 5 to 14 minutes. The October 2026 fee schedule file shows all three as status A.

The CPT codes many commercial plans use, 99408 and 99409, carry status N in the same file, meaning Medicare does not cover them. HCPCS H0015, an alcohol and drug intensive outpatient code, carries status I, not valid for Medicare. Whether a state Medicaid agency or commercial plan accepts 99408, 99409 or an H-code is that payer's choice, so read its own fee schedule.

Office-based opioid use disorder treatment has monthly codes G2086, G2087 and G2088, all status A and separate from the OTP bundles. Collaborative care codes 99492 to 99494 are on the mental health billing page.

How Does 42 CFR Part 2 Change Billing for Substance Use Treatment?

Part 2 adds a consent layer on top of HIPAA for records from a federally assisted program that holds itself out as providing substance use disorder diagnosis, treatment or referral (42 CFR 2.11 and 2.12). The definition of records includes billing information, so claims, remittances and account notes can all be covered.

A patient can sign one consent for all future treatment, payment and health care operations, and name recipients as treating providers, health plans and people who help run the program (42 CFR 2.31). It must also state the purpose, the right to revoke and an expiration.

A billing company working for a program under a written agreement binding it to Part 2 is a qualified service organization (42 CFR 2.11). The 2024 final rule (89 FR 12472, February 16, 2024) aligned many Part 2 terms with HIPAA and set a compliance date of February 16, 2026. Violations carry HIPAA penalties (42 CFR 2.3).

Do not send SUD-identifying notes to a payer the consent does not cover. Our HIPAA for billing vendors page covers the Business Associate Agreement side.

How Is ABA Therapy Billed, and Does Medicaid Cover It?

Applied behavior analysis is billed with CPT 97151 to 97158 (assessment, technician treatment, protocol modification and family guidance). Medicare sets no national fee for them: in the October 2026 fee schedule file the eight codes carry status C, which means the Medicare contractor prices them. Medicaid and commercial plans are where ABA is paid, and they differ.

For Medicaid, EPSDT (the early and periodic screening, diagnostic and treatment benefit for children under 21) requires coverage of necessary treatment to correct or ameliorate a condition, whether or not the state plan covers it for adults (42 U.S.C. 1396d(r)(5)). How a state delivers ABA is its own decision: provider types, qualifying diagnoses, authorization, hour limits, rates, and whether a managed care plan pays. We read the state manual and the plan policy first.

When a PHP or IOP bills ABA codes, Chapter 4 lists 97153 to 97158 under revenue code 0900 and 97151 and 97152 under 0918. See the Medicaid billing guide and pediatric billing.

Where Do Mental Health Parity and Collaborative Care Fit in a Claims Workflow?

Parity matters when a plan denies a program stay with a limit it does not apply to comparable medical stays. The Mental Health Parity and Addiction Equity Act (MHPAEA) generally bars group health plans and issuers from placing less favorable limits on mental health and substance use disorder benefits than on medical and surgical benefits.

CMS says the test is applied across six benefit classifications, including inpatient, outpatient and emergency, and that nonquantitative treatment limits such as prior authorization may not be more restrictive for these benefits. It does not apply to small employer group plans, other than through essential health benefits.

We log each denial that cites visit limits or preauthorization for program stays, with the plan's stated criteria, for appeals. The fuller discussion is on the mental health billing page.

How We Handle Behavioral Health Billing

We prepare institutional claims for programs and professional claims for their clinicians, checking bill type, revenue codes, condition codes, patient status, authorization and payer rules before release. Claims go out within 24 hours of charge entry, denials are worked within 48 hours, and we work to a 95% clean claim rate, inside your EHR.

Before an IOP or PHP can bill a commercial or government plan in network, the payer has to approve it. We get IOPs and PHPs approved and credentialed with commercial and government payers, at the facility level and at the individual provider level. Read how that works in our IOP and PHP credentialing section.

Our fee is a percentage of collections, shown on the pricing page. For facility billing across your programs, see hospital and facility billing. To talk through your programs, book a call.