New York State Medicaid Coverage Policy and Billing Guidance for the 2023-2024 COVID-19 Vaccines

  • Guidance is also available in Portable Document Format (PDF)

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.

This billing guidance maybe subject to change. Please continue to monitor New York State Medicaid COVID-19 vaccine guidance for updates to FFS reimbursement and/or billing instructions.

Medicaid FFS billing instructions for Hospital Outpatient Departments (HOPD), 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 FQHCs, 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 Managed Care 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 non-pharmacy 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. A current list of vaccines available through the VFC Program can be found at the following link.

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. VFC-enrolled providers are responsible for ordering and utilizing VFC stock and should not bill for a cost for a VFC-obtained vaccine to the Medicaid program.

Table 1
CPT Code Manufacturer & COVID-19 Vaccine CPT Code Descriptions Fee per Dose
90480* Immunization administration by intramuscular (IM) injection of SARS-CoV-2 (COVID-19) vaccine, single dose $40.00
91304 SARS-COV-2 (COVID-19) vaccine, subunit, recombinant spike protein-nanoparticle+Matrix-M1 Adjuvant, preservative free, 5 mcg/0.5 mL dose Cost
91318 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 3 mcg/0.3 mL dose Cost
91319 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 10 mcg/0.3 mL dose Cost
91320 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 30 mcg/0.3 mL dose Cost
91321 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 25 mcg/0.25 mL dose Cost
91322 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 50 mcg/0.5 mL dose Cost

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

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 "1" and a day supply of "1" for each dose, regardless of volume.

Table 2
NCPDP D.0 Claim Segment Field Value
436-E1 (Product/Service ID Qualifier) Enter the applicable value, which qualifies the code submitted in field 407-D7 (Product/Service ID) as a procedure code
407-D7 (Product/Service ID) Enter the administration code and/or applicable vaccine procedure code listed in Table 1
442-E7 (Quantity Dispensed) Enter the value of "1"
405-D5 (Day Supply) Enter the value of "1"
444-E9 (Pharmacist ID) Enter the pharmacist's NPI number
411-DB (Prescriber ID) Enter the dispensing pharmacy's NPI number*

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

Please see the NYS Medicaid Pharmacy Manual Policy Guidelines document for further guidance on origin code and serial number values that must be submitted on the claim for "pharmacy dispensing" when applicable for non-patient- specific orders. Enter a value of "5" in field 419-DJ (Prescription Origin Code) and a value of "99999999" in field 454- EK (Sched uled Prescription ID Number).

NCPDP D.0 Companion Guide can be found here.

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 programfor 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. VFC-enrolled providers are responsible for ordering and utilizing VFC stock and should not bill for a cost for a VFC-obtained vaccine to the Medicaid program.

Note for pharmacies not enrolled in the VFC program: Limited to the 2023-2024 vaccine season, non-VFC enrolled pharmacies may bill for the actual acquisition cost of the COVID-19 vaccine per the guidance posted here.

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. MMC Plan information can be found by visiting the following website.

Questions and Additional Information: