Remaining CDC PEPFAR Programs Face Funding Cliff

The President’s Emergency Plan for AIDS Relief (PEPFAR), a widely successful global health program, risks having its funding choked off. Since the dismantling of the United States Agency for International Development (USAID), the Centers for Disease Control and Prevention (CDC) has become the primary funder of remaining PEPFAR programs. Now, those programs face an uncertain future as the Department of State prioritizes bilateral Memorandums of Understanding (MOUs) under the America First Global Health Strategy. PEPFAR is credited with saving 26 million lives and enabling 7.8 million babies to be born HIV-free across 55 countries.

Historically, the CDC has been the second-largest implementer of PEPFAR programming within the U.S. government. According to the KFF, in FY2023, USAID was the largest implementer of PEPFAR programming, accounting for 60%, while the CDC accounted for 37%. During the 2025 dismantling of USAID, 86% of its contracts were terminated, including 71% of its global health portfolio. This shift made the CDC the largest implementer of remaining PEPFAR programs. Now, however, PEPFAR funding from the CDC is being restricted by the State Department.
This restriction stems largely from budgetary decisions at the State Department.

A recent report by Global Health Watch found that the State Department has released only $640 million of the $1.3 billion typically appropriated to the CDC for PEPFAR. Andrew Green reports in Devex that this restriction persists despite Congress authorizing the funding in 2025, due to the absence of explicit language requiring the State Department to transfer the funds. The State Department now has the role of operationalizing the America First Global Health Strategy.

According to Green, the State Department aimed to finalize bilateral MOU “deals” by December 2025 and begin implementation in April, alongside a six-month bridge plan for CDC programs. However, with only 27 deals in place, most finalized early this year, the effort is behind schedule. A New York Times report highlighted that, in the case of Zambia, the State Department is threatening to cut PEPFAR funding as a negotiating tactic. In a unique case, a leaked Zambia MOU ties PEPFAR funding to mineral access for U.S. companies, while agreements with Zimbabwe and Kenya reportedly involve the transfer of data and biological samples.

This has created a chokepoint for CDC-funded programs, which now face a funding cliff as the bridge plan ends and the State Department still works through the early stages of redesigned bilateral funding mechanisms. According to an NPR report, delays in CDC funding are likely a result of turf wars between the State Department and the CDC. Historically, PEPFAR funding passed through the State Department before being divided among USAID and CDC. Now, despite approval by Congress, PEPFAR funds remain unspent at the State Department.

This funding cliff will have real costs for millions of people suffering from the AIDS epidemic. One affected program is the Eastern Deanery AIDS Relief Program (EDARP) in Nairobi, Kenya. Founded by Maryknoll Fathers and Brothers, EDARP has served thousands of HIV-positive residents and, in recent years, prevented mother-to-child transmission of the virus in over 98% of births. In 2025, despite continued support from the CDC and Maryknoll, its annual budget fell from $3.7 million to $2.2 million. Of roughly 400 clinical staff at the start of 2025, only 191 were still employed by year’s end, and eight of its 14 clinics—more than half—have already been forced to close.

Photo: Eastern Deanery AIDS Relief Program in Kenya, recipient of PEPFAR funding, founded by the the Maryknoll Fathers and Brothers.