COVID-19 vaccines billing guide

Keeping you up to date on the latest COVID-19 vaccine developments is our top priority. We are monitoring COVID-19 vaccine updates from state and federal governments.

Effective September 11, 2023, for New York State Medicaid Fee-for-Service (FFS) and for Medicaid Managed Care (MMC) Plans, reimbursement is available to enrolled and qualified providers for COVID-19 vaccines and their administration as approved by the FDA or authorized for emergency use.

Providers are prohibited from charging Medicaid members a co-payment or any cost sharing responsibility for the COVID-19 vaccine or the administration of the COVID-19 vaccine.

Medicaid FFS billing instructions for Hospital Outpatient Departments (HORD), Free-standing Diagnostic and Treatment Centers (D&TC), School Based Health Centers (SBHC) and Federally Qualified Health Centers (FQHC)) (including School Based Health Centers designated as Federally Qualified Health Centers):

HOPDs, D&TCs, SBHCs, and FGHCs, including SBHCs designated as FQHCs (SBHC/FQHC) should bill an ordered ambulatory claim for COVID-19 vaccines and their administration using the CPT codes from Table 1 below, for individuals 19 and older.

Note: SBHCs and SBHC/FQHCs providing COVID-19 vaccines to Medicaid FFS and MMC members will be required to append the HA modifier to the appropriate vaccine and vaccine administration Current Procedural Terminology (CPT^®) code when billing Medicaid FFS.

Office based practitioners

Physicians, nurse practitioners, midwives, and group practices must bill a professional claim for COVID-19 vaccines and their administration. Claims must include the appropriate CPT code for the COVID-19 vaccine toxoid and CPT code for vaccine administration from Table 1 below, for individuals 19 and older.

Vaccines for Children Program (VFC)

COVID-19 vaccines are available through the VFC Program. The VFC Program is a federally funded program that provides vaccines at no cost to eligible children under 19 years of age. VFC vaccines are distributed to enrolled VFC providers to administer to VFC-eligible children.

NYS Medicaid will reimburse $25.10 for the administration of VFC-available vaccines to Medicaid members under 19 years of age. Medicaid will not reimburse providers for the cost of vaccines available through the VFC program.

Vaccines available through the VFC Program are subject to change. The Centers for Disease Control and Prevention (CDC) maintains a current list of VFC-available vaccines.

For Medicaid members under 19 years of age, providers must bill the appropriate CPT code for the COVID-19 vaccine toxoid administered (from Table 1 below) appended with the SL modifier, and CPT code 90460 to be reimbursed $25.10 for the administration of the vaccine.

Table 1

*Use CPT code 90480 for the administration of a COVID-19 vaccine to individuals 19 and older.

Currently approved AMA CPT COVID-19 codes

Health care professionals should use published AMA CPT codes when submitting COVID-19 vaccine administration claims.

The table below summarizes COVID-19 vaccine codes. It is adapted from the AMA website:

NYRx billing instructions for qualified pharmacies

The pharmacy must submit the claim for the vaccine and administration via the NCPDP D.0 claim format. In the Claim Segment field 436-E1 (Product/Service ID Qualifier), the applicable value for vaccine or administration will qualify the code submitted in field 407-D7 (Product/Service ID) as a procedure code. The applicable procedure code for administration or the vaccine will be submitted in field 407-D7 (Product/Service ID). Pharmacies will bill with a quantity of one and a day supply of one for each dose, regardless of volume.

Table 2

*If the vaccine is being ordered by a prescriber and not the pharmacist, please enter the prescriber’s NPI number.

Note: COVID-19 vaccines are available to members younger than 19 years of age through the Vaccines for Children (VFC) Program. Pharmacies may not bill Medicaid for the cost of vaccines that are available through the VFC program for VFC-eligible members. Pharmacies enrolled in the VFC program will submit the administration code 90460 for administration of a COVID-19 vaccine and the applicable vaccine code from Table 1 with an ingredient cost of $0.00 when providing a COVID-19 vaccine to a VFC-eligible member. Procedure code 90460 has a fee of $25.10.

Medicaid Managed Care (MMC) vaccine billing

NYRx should be billed for any COVID-19 vaccine administered by a pharmacy provider. For non-pharmacy providers, MMC reimbursement, billing, and/or documentation requirement questions should be directed to the specific MMC plan of the enrollee. 

References

2024 CPT Manual, AMA.
New York State Medicaid Coverage Policy and Billing Guidance for the 2023-2024 COVID-19 Vaccines. New York Department of Health.