New York Medicaid providers must submit claims within 90 days of the date of service, and no claim is payable if it reaches eMedNY two years or more after that date. Those two numbers set the outer boundaries of the New York Medicaid timely filing deadline. Between them sits a narrow set of exceptions: when something outside the provider’s control kept the claim from going out on time, the provider has 30 days from the point the obstacle cleared to file, and the claim must carry a numeric delay reason code explaining why it is late.1New York Codes, Rules and Regulations. 18 NYCRR 540.6 – Billing for Medical Assistance
The 90-day clock runs from the date the service was furnished, not from the date the claim is prepared or the date paperwork is signed. The rule applies uniformly across provider types and service categories under 18 NYCRR 540.6.
The Two-Year Absolute Cutoff
Even a claim protected by a valid delay exception cannot survive past two years from the date of service. Under 18 NYCRR 540.6(a)(3), claims from non-public providers must be finally submitted and payable within two years of the date of service, and public providers face the same window unless a separate agreement with the Department of Health says otherwise.2Cornell Law Institute. New York Comp Codes R and Regs Tit 18 540.6 – Billing for Medical Assistance
eMedNY enforces this automatically. Any claim received two years or more after the last effective date of service is denied outright, and there are no exceptions to the edit.3eMedNY. Managed Care – Stop Loss No delay reason code, retroactive eligibility determination, third-party processing dispute, or pending litigation will rescue a claim past that line. For any claim held up by long-running insurance disputes or litigation, the two-year date is the one to calendar.
When Late Filing Is Allowed
The regulation recognizes a defined list of situations where filing within 90 days genuinely was not possible. Every one of them triggers the same follow-on rule: the provider has 30 days from the moment filing became possible to get the claim in.4eMedNY. Submitting Claims Over 90 Days From Date of Service
Retroactive or Unknown Eligibility
When a patient’s Medicaid coverage is backdated, or when eligibility could not be confirmed on the date of service, the provider had no way to bill Medicaid at the time. The 30 days start running when the provider is notified of the patient’s eligibility.5eMedNY. Information for All Providers – General Billing
Third-Party Insurance Processing
Medicaid is the payer of last resort, so Medicare or private insurance has to be billed first. If the primary insurer takes months to adjudicate, the Medicaid claim cannot go out until that resolves. The 30-day window opens on the date the provider receives the primary insurer’s determination.
State Administrative Delays
Where the Department of Health or a local social services district causes the delay through its own processes, including delays in provider certification, prior approval, or state-directed changes to retroactive reimbursement, the provider is not penalized. The 30-day clock begins when the state notifies the provider that the issue has been resolved.4eMedNY. Submitting Claims Over 90 Days From Date of Service
Litigation and Natural Disasters
Litigation that creates the possibility of payment from another source tolls the filing deadline until the provider regains control of the billing decision. Natural disasters qualify separately under delay reason Code 15. During declared emergencies, federal authorities may issue blanket waivers under Section 1135 of the Social Security Act that temporarily modify Medicaid filing requirements.6Centers for Medicare & Medicaid Services. Waivers and Flexibilities
Delay Reason Codes and Documentation
HIPAA requires every claim submitted beyond the 90-day limit to carry a numeric delay reason code. The eMedNY-recognized codes are:4eMedNY. Submitting Claims Over 90 Days From Date of Service
- Code 1 – Proof of eligibility unknown or unavailable on the date of service
- Code 2 – Litigation that may result in payment from another source
- Code 3 – State-authorized and directed delayed submissions
- Code 4 – Delay in certifying the provider
- Code 5 – Delay in supplying billing forms
- Code 6 – Delay in supplying custom-made appliances
- Code 7 – Third-party insurance processing delay
- Code 8 – Delay in eligibility determination (backdated or changed coverage)
- Code 9 – Original claim rejected or denied for a reason unrelated to timely filing
- Code 10 – Administrative delay in the prior approval process
- Code 11 – Other
- Code 15 – Natural disaster
The code does not go on the UB-04 claim form. It is entered on a separate delay reason code form.7eMedNY. Frequently Asked Questions on Delayed Claim Submission Supporting documentation must be kept on file for six years. Useful records include the Explanation of Benefits from a primary insurer, state notifications of retroactive eligibility, prior approval correspondence, and anything else that fixes the date filing became possible.
Rejected Claims and the 60-Day Correction Window
When eMedNY returns a claim because of data errors or billing mistakes, the provider has 60 days from the date of notification to correct and resubmit it. Paid claims that need adjustment must also be resubmitted within 60 days. A claim that is still not payable after the second resubmission is no longer valid or enforceable.5eMedNY. Information for All Providers – General Billing
This is where reimbursement most often gets lost. A claim filed on day 89 that comes back rejected still has 60 days to be fixed, even though the original 90-day window has closed. But a rejection notice that sits unread until day 61 kills the claim. Rejections need to trigger action the moment they arrive, tracked separately from initial filing dates.
Managed Care Plans Set Their Own Rules
Most New York Medicaid beneficiaries are enrolled in managed care rather than fee-for-service Medicaid. Many managed care organizations use the same 90-day initial filing deadline, but each plan sets its own filing requirements in its provider manual, and some impose shorter deadlines or different documentation rules for late claims. Before assuming the fee-for-service timeline applies, check the plan’s provider manual for the claim in front of you.
The two-year absolute deadline still governs managed care claims processed through eMedNY, including stop-loss payments. Any managed care claim submitted two years or more after the last effective date of service is denied automatically, with no exceptions.3eMedNY. Managed Care – Stop Loss
If a Claim Is Denied on Timeliness Grounds
For fee-for-service claims denied through eMedNY, start with the denial reason on the remittance advice. If the denial reflects a data error or missing information, the 60-day resubmission window governs. If the denial was based on timely filing and a valid delay exception should have applied, the claim can be resubmitted with the correct delay reason code and supporting documentation, provided the two-year outer limit has not passed.
For managed care denials, providers have an independent right to file an internal appeal with the plan. Plans must allow at least 45 days to file a utilization review appeal, though the exact timeframe varies and should be confirmed in the plan’s provider manual. If the internal appeal ends in a final adverse determination, the provider can request an external appeal within 60 days of that notice when the plan denied authorization or payment on medical necessity, experimental, or coverage-criteria grounds. Providers do not have an independent right to request a state fair hearing; that right belongs to the Medicaid enrollee.