Navigating the 2025 Continuing Resolution: What Free and Charitable Clinics and Charitable Pharmacies Need to Know

Puzzle collage of US Capitol Building, Capitol Hall, Patients in Waiting Room, and Patient Room

Overview

On March 15, 2025, President Trump signed a continuing resolution (CR) to prevent a government shutdown, extending federal funding through September 30, 2025. The bill grants President Trump and the Department of Government Expenditures (DOGE) greater control over federal spending.

While the CR generally maintains funding levels from fiscal year 2024, it includes key changes such as increased defense and immigration enforcement spending and reductions in some non-defense areas. Healthcare funding remains relatively stable, with US global health funding at $10.8 billion and funding for the CDC, NIH, and other health agencies consistent with FY2024 levels. However, concern remains over the lack of agency direction on fund allocation, and the budget for healthcare and other essential services beyond September 30, 2025

remains a question in the face of threatened cuts.

Key Policy Highlights for the Healthcare Safety Net Health Funding

The CR provides advanced funding through the first quarter of fiscal year 2026 for key health programs, including:

• $261 billion in Medicaid payments to states

• Extended health programs through September 30, including:

  • Medicare payments to Disproportionate Share Hospitals (DSH), which serve large numbers of Medicaid and uninsured patients

  • Expanded Medicare telehealth coverage, including for Rural Health Clinics (RHCs) and Federally Qualified Health Centers (FQHCs)

  • Funding for the Community Health Center Fund

  • Temporary Assistance for Needy Families (TANF)

  • Continued support for FQHCs, the National Health Service Corps, and teaching health centers

  • Extension of the special diabetes program for Type I diabetes

    
    

Food Security

• Supplemental Nutrition Program for Women, Infants, and Children (WIC): Increased funding by over $500 million to a total of $7.59 billion

• Commodity Supplemental Food Program (CSFP): No funding increase, potentially impacting low-income seniors

• Emergency Food Assistance Program (TEFAP): No additional funding for food banks and pantries

• Unemployment Insurance: $3.9 billion allocated from the Unemployment Trust Fund for state grants

  
  

Housing

• Tenant-Based Rental Assistance Program: Increased by $3.65 billion but insufficient to cover voucher renewals, leading to an estimated 32,000 lost vouchers

• Project-Based Rental Assistance Program: Increased by $880 million

• Affordable Housing Programs:

  • Section 202 (housing for older adults): Increased by $18.4 million

  • Section 811 (housing for people with disabilities): Increased by $48.7 million

  • Community Development Fund: Decreased by $3.29 billion

  • Homeless assistance programs face potential $168 million shortfall due to funding repurposing

  • HUD’s Healthy Homes and Fair Housing programs remain level-funded

    
    

Impact on Federal Grant-Making Processes

The CR introduces delays and uncertainty into the grant-making process, impacting federal agencies and nonprofits reliant on federal funding. Key agency-specific challenges include:

• HHS: Workforce reductions, including $25,000 buyouts, will slow down grant processing and management.

  • HRSA: Significant reductions in funding for healthcare facilities and training grants.

  • NIH: Ongoing disruptions due to grant cancellations and research office closures.

  • SAMHSA: Potential staff reductions of up to 70%, office closures, and delays in grant competitions.

• Education Department: Cancellation of $1.5 billion in grants, including teacher training programs and research contracts.

• HUD: Mixed funding impacts with some increases but overall operational challenges.

• USDA: Competitive grant programs face funding freezes, cancellations, and leadership voids affecting grant administration.

  
  

Funding Uncertainties and Adaptation Strategies

The $15 billion cut to non-defense discretionary spending will reduce available grants, increase competition, and create operational challenges not only for federal grant recipients but for state and local agencies that may subaward this funding to community organizations. Free and Charitable Clinics and Charitable Pharmacies work closely with other partners, including food assistance and housing assistance programs, to take care of their patients and any break downs in the system can adversely impact the care we provide. To navigate these changes, Free and Charitable Clinics and Charitable Pharmacies and their partners in the healthcare safety net should consider:

• Diversifying funding sources to absorb potential reductions in funding from traditional sources

• Internal assessments to identify ways to streamline workflows and optimize efficiency

• Community assessments to stay on top of the needs of patients and partners in this ever-changing landscape

• Enhancing communications to maintain credibility with funders and donors

• Engaging in advocacy efforts to influence funding and policy decisions

MaryCatherine Jones Consulting, LLC provides grant research and writing assistance, as well as overall capacity building support, including training, strategic planning, and program evaluation. You don’t have to go through this alone.  

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Final Thoughts

The 2025 continuing resolution has not eased uncertainty in the charitable healthcare sector. Cuts to non-defense discretionary funding will likely create operational challenges for local and state partners, requiring strategic planning and adaptability. If you need support navigating these changes, don’t hesitate to reach out—we’re here to help.

Thanks to those who have shared insights on specific program impacts. Free and Charitable Clinics and Charitable Pharmacies have overcome tough times before, and by staying informed and connected, we can weather these changes together.