As he does every three months, Sibusiso traveled on Wednesday morning to a clinic in the capital of Eswatini, a tiny southern African nation, to get a refill of the H.I.V. medication he needs to save his life. When he arrived, the door was locked and about 20 other patients stood outside, baffled that the clinic was closed.
Sibusiso, 39 and unemployed, had heard rumors that President Trump was pulling funding for the program that supported his treatment. Now, though, he learned the reality: The Trump administration had ordered a halt to the President’s Emergency Plan for AIDS Relief, or PEPFAR, one of America’s most consequential aid programs in Africa.
The abrupt pause of a $6.5 billion program established by former President George W. Bush and credited with saving the lives of tens of millions of people sent patients, clinicians and public health advocates across Africa into a panic. Many feared a return to some of the darkest days on the continent, when H.I.V. spread rapidly and a diagnosis was akin to a death sentence.
As Sibusiso stood outside the clinic, he feared he could be next. He had taken the last of his antiretroviral medication that morning. And even though the Trump administration had backtracked, suddenly announcing on Tuesday that lifesaving medications and treatments could continue to be distributed, the clinic remained shuttered in the confusion.
Sibusiso, standing outside, had no idea where or when he could get more medicine.
“I’m now thinking of dying,” said Sibusiso, who requested that only his first name be used to protect his privacy. “What am I going to do without this treatment?”
The Trump administration has said that foreign assistance programs will be paused for three months as it reviews how money is being spent. If the administration decides to end PEPFAR, it could lead to 600,000 deaths over the next decade in South Africa alone, where the program has its largest number of beneficiaries, according to a study.
“The next 90 days are looking so dystopian,” said Nozizwe Ntsesang, the chief executive of a leading gay rights advocacy group in Botswana.
Across South Africa and other countries in the region, fear and uncertainty are palpable. Some African leaders had shared optimism and excitement about a second Trump term. But now, one of his first moves appeared to put lives at risk.
“I’m scared,” said a 19-year-old South African college student who was born with H.I.V. “People will die. It’s going back to the ’90s where people did not have enough medication to treat the disease.”
The student, who also requested anonymity to protect her privacy, said the clinic that she goes to in Johannesburg gave her a three-month supply of her antiretroviral medication on Wednesday instead of the usual six months. Officials explained that they wanted to reserve some stock in case other clinics ran short, she said.
PEPFAR does not provide medication for the South African health system, but it does employ around 13,000 medical professionals, from doctors to community health workers, who are responsible for ensuring that people are tested and seek proper treatment. Virtually all of those employees were ordered to stop working after the Trump administration froze foreign aid programs, according to health care advocates.
The staff shortages, health workers and rights groups said, led to much larger crowds at public clinics in South Africa, where roughly eight million people are living with H.I.V. and 5.7 million receive treatment.
Amid the chaos of the freeze and the Trump administration’s backpedaling, many clinics remained shuttered on Wednesday, with medical workers unsure about the new rules and patients frantic to secure their medication.
Some patients have been forced to wait 10 hours for treatment, advocates said. There were also fears that, without counselors to talk to, some patients, especially those newly diagnosed with H.I.V., would not administer their treatments properly or seek help in the future.
“The abrupt stop is not responsible,” said Solange Baptiste, the executive director of the International Treatment Preparedness Coalition, an organization that works to improve access to treatment for people with H.I.V. “Lives are at risk when you do that.”
South Africa is in a better position than many other African countries. The government procures most of its H.I.V. drugs directly and relies on PEPFAR for only about 17 percent of its overall H.I.V. treatment budget.
Neighboring Botswana, which has received nearly $72 million in aid from PEPFAR since 2003, also buys its own treatment medication, but the work and funding stoppage has weighed heavily on local organizations.
Stanley Monageng said he cried when he learned about the Trump administration’s order. Mr. Monageng, 78, has been running an organization in Molepolole, in southern Botswana, since 2005. It provides support for children with H.I.V. and relies mostly on PEPFAR funding, he said.
Mr. Monageng said he was worried all week that he would not be allowed to provide antiretroviral medication to the dozens of children, many of them orphaned, who rely on his organization for help. Mr. Monageng himself has been living with H.I.V. for 25 years and says he has personally benefited from the PEPFAR program.
“I asked myself, ‘How are these orphans going to survive? How am I going to help them?’” he said on Wednesday from the three-bedroom house that he uses for the center. “I’ve been surviving all these years because of America.”
At HealthPlus 4 Men, the clinic that was closed in Eswatini on Wednesday, officials encouraged anxious patients to go to a public hospital to seek medication. But most patients were uncomfortable with that option.
HealthPlus primarily treats gay men, a population that has been historically stigmatized in Eswatini. Many of its patients fear going to government-run facilities, where they worry they will face discrimination. Public hospitals also often provide prescriptions that many patients can’t afford to fill, said Sibusiso Maziya, the executive director of HealthPlus.
“It’s a sad moment for us,” Mr. Maziya said. “They want to know when this situation will change, when are we opening.”
Despite the waiver issued by the U.S. government on Tuesday, Mr. Maziya said his organization was continuing to withhold antiretroviral medication supplied with PEPFAR funds as it awaits clarity from its funders on what it is allowed to do.
Msizi Mkhabela, the operations manager for HealthPlus, added that the organization promotes diversity, equity and inclusion by supporting equal treatment for gay men. That mission could run afoul of the Trump administration’s freeze on such programs and may put the clinic at a higher risk of being permanently defunded.
In addition to medication, HealthPlus also has a mobile clinic and outreach programs to make sure that people living in rural areas are being tested and receive treatment for H.I.V. The organization considers those programs an essential part of its efforts to prevent the spread of the disease. But all of that was put on hold because the funding came from PEPFAR and HealthPlus is unsure what activities are allowed to continue.
“We are literally shaking and worried,” Mr. Mkhabela said. “Very much frustrated.”
Reporting was contributed by Yvonne Mooka from Molepolole, Botswana, Lynsey Chutel from London and Golden Matonga from Blantyre, Malawi.
