As Fiscal Year Deadline Looms, U.S. Faces Foreign Aid Fight and Public Health Upheaval

Sep 15, 2025

With the fiscal year set to close in just weeks, the U.S. is confronting two escalating crises: a battle over billions in foreign aid and medical research funding, and upheaval at the nation’s top public health agency, including vaccine policy. Together, they mark the latest turn in an eight-month dismantling of U.S. global health and public health leadership. On one front, the Trump administration is pressing to withhold billions in foreign aid and slash medical research, setting up a constitutional showdown with Congress and the Supreme Court. On the other hand, the CDC has been plunged into turmoil after the ouster of its director, high-level resignations, and rapidly shifting vaccine policies under Health Secretary Robert F. Kennedy Jr. The twin crises have created an unprecedented moment of uncertainty, with billions in global health funding and the credibility of U.S. public health institutions hanging in the balance.

Budget Battles at a Glance

Foreign aid showdown: The Trump administration’s $5B “pocket rescission” faces a legal battle after a lower court ordered $4B released by Sept. 30. Chief Justice John Roberts issued a temporary stay while the Supreme Court weighs the case, with the Government Accountability Office (GAO) deeming the maneuver unlawful and aid groups, including the Global Health Council, pressing for enforcement.
NIH funding and spending: House Republicans blocked a 40% NIH cut, holding the budget flat at ~$48B. NIH has surged in August and is now on track to use nearly all of its $47B appropriation by Sept. 30—though far fewer new projects are being funded. At the same time, the Supreme Court allowed $783M in DEI-linked NIH grant cuts.
HIV prevention pledge: The U.S. committed to deliver Gilead’s lenacapavir, a twice-yearly injectable, to 2M people by 2028 via PEPFAR. While hailed as a breakthrough, concerns linger over delivery, access, and whether it offsets broader cuts to HIV and global health programs.
Critical date: Sept. 30 marks the close of the fiscal year—and the deadline for multiple unresolved funding battles to collide.

The U.S. budget process—already a high-stakes arena—has become a defining battleground over the future of foreign aid and global health. Over the summer, the Trump administration dismantled USAID, canceled most projects, and rescinded $8 billion in assistance. In late August, it went further, proposing a controversial $5 billion “pocket rescission” designed to let funds expire at fiscal year’s end without congressional approval.

The legality of this maneuver, which GAO has deemed unlawful—a rare instance of independent oversight pushing back on the administration—has sparked a legal maelstrom. A federal judge ordered the administration to release $4 billion to aid groups by September 30. Last week, Chief Justice John Roberts issued a temporary administrative stay, putting that order on hold while the Supreme Court considers the case. On September 12, aid groups, including the Global Health Council, filed opposition, urging the Court to enforce the lower court’s ruling. The stakes are high: a decision could fundamentally reshape whether Congress or the presidency ultimately controls U.S. foreign aid spending.

Meanwhile, Congress and the administration are clashing over health research. House Republicans rejected the White House’s call for a 40% NIH cut, advancing a bill that holds funding flat at ~$48 billion. Yet the Supreme Court has already permitted the administration to cut $783 million in NIH grants tied to diversity, equity, and inclusion programs—jeopardizing more than 1,700 projects with global health relevance, from infectious disease research to minority and LGBTQ+ health equity.

At the same time, the NIH itself has scrambled to meet spending deadlines. After falling behind earlier in the year due to grant evaluation pauses, staffing cuts, and extra political review, the agency surged in August and now appears on track to use nearly all of its $47 billion appropriation before the fiscal year ends on September 30. As of mid-September, NIH has awarded about $31.2 billion in both new and continuing grants—slightly ahead of the historical average. However, despite catching up on total spending, NIH is still funding far fewer new projects, signaling that many opportunities have been foregone.

Against this turbulent backdrop, the U.S. announced a new global HIV prevention initiative: a PEPFAR-led commitment to provide Gilead’s lenacapavir, a twice-yearly injectable drug, to 2 million people by 2028. Gilead Sciences will supply the drug “at no profit.” Advocates welcomed the innovation, especially for preventing mother-to-child transmission, but raised concerns about logistics, access, and whether the move offsets broader cuts to U.S. HIV and global health programs.

Together, these developments highlight a period of deep uncertainty, with billions for foreign aid, medical research, and humanitarian programs hanging in the balance. The next flashpoint will come at the end of September, when the fiscal year closes and unresolved funding battles collide with urgent deadlines.

HHS Leadership & Vaccine Turmoil

Leadership upheaval: CDC Director Susan Monarez was removed just weeks after Senate confirmation; three senior leaders resigned. A shooting at CDC headquarters on Aug. 8 added to the turmoil.
Political interference: Health Secretary RFK Jr. has reversed vaccine recommendations, dismantled advisory panels, and elevated vaccine-skeptical appointees—moves critics say undermine credibility and morale.
Congress divided: At a September hearing, senators grilled Kennedy over vaccine policy. Meanwhile, House appropriators protected $1.1B for BARDA research, including mRNA vaccines, despite HHS canceling 20+ contracts worth ~$500M.
States charting their own course: California, Oregon, and Washington revived their Western Health Alliance to coordinate policy independently. Florida shifted vaccine guidance in another direction, while Northeastern states are issuing their own standards—underscoring fractured national leadership.
Global health impact: The disarray at CDC and HHS threatens public trust at home and risks weakening U.S. leadership in global health.

The Centers for Disease Control and Prevention is facing profound upheaval after the abrupt removal of Director Susan Monarez—just weeks after her Senate confirmation—the resignations of three senior officials, and a shooting at CDC headquarters in Atlanta on August 8. Public health advocates and former leaders warn these crises reflect mounting political interference under Health Secretary Robert F. Kennedy Jr., who has reversed long-standing vaccine recommendations, dismantled advisory panels, and elevated vaccine-skeptical appointees. Critics say morale is collapsing and U.S. credibility in global health is at risk.

The turbulence has spilled into Congress. At a September Senate hearing, Kennedy was grilled over his handling of vaccine policy and the sidelining of scientific expertise. While he defended his actions as reforms, lawmakers voiced concern that political directives are undermining trust in public health institutions. Meanwhile, House appropriators moved in the opposite direction, protecting vaccine innovation with $1.1 billion for advanced research at BARDA, specifically including mRNA technology—even as HHS canceled more than 20 contracts worth roughly $500 million.

States are now stepping in to fill the void. California, Oregon, and Washington revived their Western Health Alliance, first formed during the pandemic, to coordinate vaccine policy independently of federal guidance. Florida has shifted its vaccine policies in another direction, while several Northeastern states are issuing their own guidance as well. Governors across these regions cite rapidly changing federal recommendations under Kennedy as a threat to public trust, pledging to uphold science-based approaches. Together, these developments underscore the volatility of U.S. public health leadership, with ripple effects for both domestic confidence and global health engagement.

(See Sources below)

Resources

Advocacy and Mobilization

Alliance members CUGH (here and here), DNDi, For Our Health (here and here), Friends of the Global Fight (here and here), GAIA (here and here), Global Health Corps (here and here), Global Health Council (here and here), Global Health Technologies Coalition (here and here), IDEO.org (here and here), Maya Health Alliance | Wuqu’ Kawoq, MedShare, Nexleaf Analytics (here and here), North Carolina Global Health Alliance (here and here), PATH (here and here), Pathfinder (here and here), Population Services International (here and here), ReSurge International, Seed Global Health (here and here), San Francisco Community Health Center (here and here), Stanford (here and here), UC Berkeley (here and here), UCGHI, UCSF (here and here), and UNICEF (here and here) have spoken with the press or issued statements.
Find and Contact Your Representatives: U.S. House of Representatives and U.S. Senate. Here is a list of key decision makers in Congress, their contact information, as well as sample language to consider.

Navigating the Legal Questions and Resources for Workers

Humentum offers resources for navigating the foreign assistance pause.
Connective Impact has launched an open-source resource document in response to the U.S. foreign aid policy shifts.
Devex has summarized 5 rapid response funds for organizations affected by the US aid freeze.
Just Security has a Litigation Tracker: Legal Challenges to Trump Administration Actions.
Tech Change is sharing a job board and resource curation for those impacted.
Other job opportunities sites include: Philanthropy News Digest, Idealist.org, WorkforGOOD, FastForward, Reconsidered, The Impact Job, ExecSearches.com, and Foundationlist.org.
Find a Job I Devex
The Pivot Playbook
Find and Fund Defunded Global Health Grants: database of defunded NIH global health research projects seeking support
Founders Pledge: Nonprofit organization that works to bridge the gap between entrepreneurs and charities making impact in the world

Tracking Impact

The Impact Metrics Dashboard (Boston University) visualizes the human impact of funding changes for aid and support organizations. The site has an impact tracker for PEPFAR, tuberculosis (TB), and Medicaid and is looking for additional collaborators. Read more.
GHTC tracks how US investments in global health R&D are paying economic and health dividends in each state. (Learn more)
Also see Center for Global Development I How Many Lives Does US Foreign Aid Save?
KFF has a new series of fact sheets on the status of U.S. global health aid cuts, from maternal and child health to TB and malaria, and fact sheets on global health program impact.
KFF also has an overview of President Trump’s executive actions on global health and a timeline of events that provides a detailed overview of actions (and counter-actions) related to the administration’s efforts to freeze all U.S. foreign aid and dissolve USAID.
Grant Watch’s Weekly Terminated NIH Grants Report presents an overview of recent trends in NIH grant terminations, reinstatements, new grant initiations, and continuations.
An overview of the last 30 days of what has happened to public health and a running list of actions by the Trump administration to undermine public health. [Jessica Knurick]
Emory Rollins Public Health has shared data showing the impact of public health cuts.
Devex Court Watch: The latest on the USAID docket
Devex ‘The Trump Effect’, highlighting the latest news, in-depth analysis, and exclusive insights on how the Trump administration’s policies are reshaping global development.
Gates Foundation I Health Aid Saves Lives. Don’t Cut It, provides an aggregation of US aid cut impacts
ProPublica I Gutted: How Deeply Trump Has Cut Federal Health Agencies
Verified and Vetted Science Accounts to Start Following for Public Health Accuracy [Cate Russel]