COVID-19 has not only been a clinical crisis, it has been a sustained financial stress test for independent practices, health systems, and billing companies. One persistent challenge is how to handle reimbursement for uninsured patients who received COVID-19 testing and treatment while federal relief programs have been opened, paused, and modified over time.
Many organizations left significant dollars uncollected because eligibility was unclear, coding changed repeatedly, and workflows were never fully standardized. For revenue cycle leaders, that translates into preventable write‑offs, higher denial rates, and extra rework at a time when staffing is already stretched.
This article walks through a structured, operations-focused approach to optimizing reimbursement under the HRSA COVID-19 Uninsured Program and related federal guidance. It is written for practice administrators, hospital RCM executives, and billing company owners who need an end‑to‑end view: from verifying uninsured status and coding correctly, to submitting clean claims and monitoring payment performance.
1. Understanding the HRSA COVID-19 Uninsured Program and Its Financial Impact
The HRSA COVID-19 Uninsured Program was designed to reimburse providers at Medicare rates for COVID-19 testing, testing-related services, treatment, and later vaccination for patients without health coverage, subject to available federal funding. For many organizations, these claims represented a material volume of encounters at the height of the pandemic and during subsequent surges.
From a revenue cycle standpoint, this program did three important things:
- Converted what would have been charity or bad debt into reimbursable encounters, if coded and submitted correctly.
- Shifted payer mix dynamics for emergency departments, urgent care centers, FQHCs, and hospital outpatient clinics with high uninsured volumes.
- Introduced a new “payer” with its own rules and technical requirements, adding complexity for registration, coding, and billing teams.
When HRSA reimbursement is mishandled, the impact is straightforward and negative:
- Lost revenue for encounters that should have paid at Medicare rates.
- Higher denial and rejection rates, especially for eligibility and coding errors.
- Increased staff time spent on research, corrections, and resubmission, eroding net yield.
Given tight margins and ongoing payer pressure, even a modest volume of missed or underpaid uninsured COVID-19 claims can translate into six or seven figures of lost revenue over several years for mid‑size and large organizations. This is why RCM leaders should treat HRSA uninsured billing like any other strategic payer line, not as a one‑off exception.
2. Building a Clear Eligibility and “Uninsured” Determination Workflow
Reimbursement under the HRSA program hinges on one gating question: is the patient truly uninsured according to federal criteria, and has the provider properly documented that status? The definition is narrower and more operationally demanding than simply “no card on file.”
From an RCM and patient access perspective, you need a repeatable workflow that answers four questions for every potentially eligible encounter:
2.1 Operational definition of “uninsured”
A patient is considered uninsured for HRSA purposes if there is no coverage under:
- Individual commercial or exchange plans.
- Employer-sponsored plans.
- Federal programs such as Medicare, Medicaid, CHIP, TRICARE, or VA.
- Any other liable payer or policy that would reimburse COVID-19 testing or treatment.
Many early denials were triggered because another payer existed and should have been primary, or because Medicaid-eligible individuals had not yet been screened or enrolled. Your policies should reflect that HRSA is a payer of last resort for these encounters.
2.2 Practical steps for front-end teams
To reduce risk and rework, design a front-end workflow that incorporates:
- Standardized uninsured attestation captured at registration or check‑in, including direct questions about current coverage and recent employment-based insurance.
- Real-time eligibility checks across commercial and government payers using your clearinghouse or RTE tools, even for walk‑ins.
- Basic Medicaid screening for patients who may be eligible in emergency or inpatient scenarios, especially in states with expanded COVID-19 provisions.
- Clear documentation of the date and result of eligibility checks in your EHR or practice management system.
RCM leaders should define a short exception list for cases where coverage is unclear at the point of service, then route those encounters to a specialized back‑end team within 24 to 48 hours. The key objective is to either identify a billable payer or correctly classify the encounter for HRSA submission before coding and billing start.
3. Coding COVID-19 Testing and Treatment Encounters Correctly
Even if eligibility is confirmed, improper diagnosis or procedure coding will prevent HRSA reimbursement. Coding for COVID-19 has evolved over time, with changes to ICD-10 diagnosis codes, CPT/HCPCS testing codes, and vaccine administration codes. Practices that did not keep pace with these updates saw higher denial rates and manual rework.
3.1 Diagnosis coding logic for testing and treatment
Accurate assignment of diagnosis codes is critical because HRSA requires that COVID-19 be either the primary diagnosis or clearly linked to testing-related services. RCM leaders should ensure coders use a clear decision tree, such as:
- Confirmed COVID-19 infection documented by the provider is coded with the appropriate COVID-19 diagnosis code as primary, plus secondary codes for complications or manifestations.
- Testing-related encounters without confirmed infection use exposure or screening codes that distinguish between suspected exposure that was ruled out, confirmed exposure, and asymptomatic screening.
- Pregnant patients require obstetric codes to properly signify infection during pregnancy, with COVID-19 as secondary, consistent with official ICD-10 guidance.
Coders must be trained to follow CMS and CDC COVID-19 coding updates across dates of service, rather than using a single static rule. Internal audit findings should be fed back as targeted education for high-volume specialties such as emergency medicine, primary care, and hospitalist services.
3.2 Procedure coding for tests, specimen collection, and treatment
HRSA follows Medicare rules closely, so revenue integrity teams must pay attention to:
- Correct selection of CPT and HCPCS codes for molecular tests, rapid antigen tests, antibody tests, and lab panel codes.
- Appropriate use of HCPCS specimen collection codes for drive‑through testing, nursing home collection, and outreach programs.
- Inpatient and outpatient treatment services coded with standard E/M, infusion, ventilator, and procedure codes, but linked to COVID-19 diagnoses where clinically appropriate.
- Correct vaccine and vaccine administration codes once vaccines entered the market and became reimbursable through federal channels.
Given the volume and variability of these encounters, RCM teams should deploy internal coding edits or work queue rules that flag COVID-19 claims missing required linkages between diagnosis and procedure codes. That front‑end edit layer is far cheaper than repeated denials and resubmissions.
4. Designing a Clean Claim Submission Process for HRSA
The HRSA COVID-19 Uninsured Program is highly sensitive to technical claim quality. Unlike commercial payers that may allow corrected claims, this program expects “first‑time right” submissions, and does not process interim bills, late charges, or traditional appeals in the same way. A clean claim mindset is therefore essential.
4.1 Core elements of a clean HRSA claim
RCM leaders should ensure that every HRSA-bound claim consistently includes:
- The designated HRSA payer name and payer ID in your practice management or hospital billing system, correctly mapped through the clearinghouse.
- The program-specific temporary member ID assigned to the uninsured patient via the HRSA portal, with dates of service that fall fully within the ID’s validity window.
- Accurate provider enrollment information, including NPIs and tax IDs that match what was submitted during program registration.
- The correct claim format 837P for professional services and 837I for facility and hospital claims, following Medicare-like data requirements.
Before scaling volume, most organizations benefit from a small “pilot” phase, sending test batches and reviewing all acknowledgments, rejections, and payment details with billing and IT teams. This reduces the risk of systemic mapping errors that might affect thousands of encounters.
4.2 Timeframes and filing limits
Federal guidance established filing deadlines, typically 365 calendar days from the date of service or admission. In practice, RCM teams should target much shorter internal timelines, such as:
- Coder completion within 3 to 5 days of discharge or visit.
- HRSA claim creation within 7 to 10 days of visit for outpatient, 10 to 14 days for inpatient.
- Follow‑up on any rejections or clearinghouse errors within 3 to 5 days of receipt.
These internal targets protect against backlogs, vacations, and system outages that might push filing dates close to the federal limit. They also help maintain predictable cash flow from this payer source, which typically issues payment within 7 to 10 business days after claim adjudication when funding is available.
5. Aligning Front-End and Back-End Teams Around COVID-19 Uninsured Workflows
Most HRSA problems trace back to fragmentation between patient access, coding, billing, and IT. COVID-19 uninsured encounters often begin in chaotic settings such as ED triage, pop‑up clinics, community testing events, or telehealth visits. If workflows are not coordinated, key data points can be lost before the billing team even sees the account.
5.1 Practical cross-functional alignment steps
RCM leaders can protect revenue and reduce rework by implementing a coordinated operating model built around four pillars:
- Standard operating procedures for uninsured registration, eligibility checks, and HRSA classification that are shared across registration, ED, urgent care, and telehealth teams.
- Shared checklists for coders and billers that specify the diagnosis/procedure combinations considered “HRSA ready,” along with any required documentation in the note.
- Dedicated uninsured or HRSA work queues in the EHR and billing system, so that these encounters can be routed to specialized staff who understand the nuances.
- Regular cross‑department reviews where front-end and back-end leaders jointly review denials, rejections, and missing data patterns, then adjust forms or scripting.
An example: if you discover that HRSA claims from a drive‑through testing site frequently lack proper exposure or screening diagnoses, the solution is not just coder education. It is also redesign of the registration template and provider documentation prompts used in that location.
5.2 Metrics and KPIs to track operational health
At minimum, your revenue cycle dashboard for COVID-19 uninsured encounters should include:
- Volume of HRSA‑eligible encounters by location and service line.
- Percentage of eligible encounters actually billed to HRSA vs written off as charity or bad debt.
- First-pass acceptance rate at the clearinghouse and HRSA portal.
- Denial and rejection rates by top reason code, segmented into eligibility, coding, and technical errors.
- Average days to payment from date of service and from claim submission.
RCM leaders should review these metrics monthly. Any trend of rising denials or slipping first‑pass acceptance suggests a process breakdown such as new staff, code changes, or configuration issues after a system upgrade.
6. Managing Program Changes, Funding Constraints, and Audit Risk
Unlike stable commercial contracts, HRSA COVID-19 funding has been subject to federal budget decisions, program pauses, and evolving rules. That creates three distinct risk categories for providers.
6.1 Funding availability and revenue forecasting
Funding for the uninsured program has at times been temporarily exhausted, leading to pauses in accepting new claims. Revenue cycle leaders should treat HRSA as a volatile line in payer mix analysis and scenario planning. Sensible actions include:
- Scenario modeling with and without HRSA reimbursement for projected uninsured COVID-19 volume.
- Communication with finance and service line leaders when policy changes are announced, so that expectations can be managed.
- Contingency planning that clarifies how uninsured COVID-19 encounters will be handled if reimbursement is no longer available, for example shifting to charity care policies.
6.2 Documentation integrity and audit readiness
Because HRSA is a federal program that pays at Medicare rates, it carries audit exposure similar to other federal payers. Revenue cycle and compliance teams should ensure that:
- Eligibility documentation and uninsured attestations are retained in the record.
- Clinical documentation supports COVID-19 diagnoses and testing indications as coded.
- Charge capture accurately reflects services provided, with no upcoding of E/M or procedures.
- Any internal or external audit findings are remediated with focused training and policy updates.
Implementing periodic internal sample audits of COVID‑19 uninsured claims is a low‑cost way to identify patterns that might attract attention in a formal review. This is especially important for high-volume emergency departments and outpatient testing clinics.
7. When and How to Leverage External Billing Expertise
For many independent practices and smaller hospitals, the COVID-19 uninsured program represented an unusual and technically demanding payer, layered on top of existing staffing shortages and competing RCM priorities. Billing companies and outsourced RCM partners can play a useful role if engaged thoughtfully.
Situations where external expertise is often justified include:
- Significant backlog of uninsured COVID‑19 encounters approaching filing limits.
- High denial rates driven by technical errors that internal IT and billing teams cannot resolve quickly.
- Limited internal coding depth for evolving COVID-19 code sets and payer policies.
- Multi‑entity or multi‑state organizations with inconsistent processes across locations.
If your organization is looking to improve billing accuracy, reduce denials, and strengthen overall revenue cycle performance, working with experienced RCM professionals can make a measurable difference. One of our trusted partners, Quest National Services, specializes in full‑service medical billing and revenue cycle support for healthcare organizations navigating complex payer environments, including evolving COVID‑19 reimbursement requirements.
Regardless of whether you keep this function in‑house or partner externally, the core management responsibilities remain the same. You still need clear governance, KPIs, and accountability for timely submission, denial management, and compliance oversight for HRSA uninsured claims.
8. Turning COVID-19 Uninsured Billing Into a Repeatable RCM Capability
COVID‑19 focused programs may eventually sunset, but the underlying challenges they revealed are not going away. Payer rules will continue to change quickly, new public health programs will emerge, and uninsured or underinsured patients will remain a constant feature of the U.S. healthcare landscape.
Organizations that treat the HRSA COVID-19 Uninsured Program as a one‑time anomaly will miss the opportunity to build durable capabilities in front‑end eligibility, coding agility, clean claim engineering, and cross‑functional alignment. Those that take a more strategic view can reuse the same frameworks for future initiatives, whether related to pandemics, new vaccine campaigns, or disease‑specific public health funding.
The path forward for RCM leaders includes:
- Embedding uninsured eligibility decision trees and attestation workflows into your standard patient access playbook.
- Maintaining a central coding intelligence function that monitors federal guidance and pushes frequent, targeted updates to coders and providers.
- Using HRSA experiences to harden your clearinghouse configurations, edit logic, and denial analytics capabilities.
- Institutionalizing cross‑department reviews any time a new payer program or funding stream is introduced.
Handled well, COVID-19 uninsured billing can shift from a source of uncertainty to a demonstration of your organization’s ability to adapt quickly while protecting cash flow and compliance.
If you want help assessing your current COVID‑19 uninsured workflows, quantifying potential missed reimbursement, or designing a more resilient revenue cycle for future public health programs, you can contact our team. A focused review of eligibility, coding, and claim submission processes often reveals fast, actionable improvements that translate directly into recovered revenue and reduced denials.
References
(Note: Always confirm the latest federal and payer guidance, as policies and codes evolve.)
- Centers for Medicare & Medicaid Services. (n.d.). COVID-19 frequently asked questions (FAQs) on Medicare fee-for-service (FFS) billing. Retrieved from https://www.cms.gov
- Centers for Disease Control and Prevention. (2021). ICD-10-CM official coding guidelines: Coding encounters related to COVID-19. Retrieved from https://www.cdc.gov
- Health Resources & Services Administration. (n.d.). COVID-19 claims reimbursement to health care providers and facilities for testing, treatment, and vaccine administration for the uninsured. Retrieved from https://www.hrsa.gov
