A single dose of an experimental drug cured malaria in 96.8 percent of children treated in a large trial in Mozambique, Kenya and Burkina Faso, matching the standard three-day treatment and clearing the way for what researchers say could be the biggest change in malaria care in two decades.

The drug, ganaquine, was tested in 3,400 children aged 6 months to 12 years with uncomplicated malaria, the researchers reported on Thursday at a tropical medicine conference in Maputo. The cure rate 28 days after treatment was statistically equivalent to the 94.1 percent achieved with artemether-lumefantrine, the twice-daily combination pill that has been the backbone of malaria treatment since the early 2000s. Ganaquine, developed by a nonprofit drug partnership with a Swiss manufacturer, kills the parasite through a mechanism unrelated to artemisinin, the compound to which resistance has emerged in Southeast Asia and, in recent years, in East Africa.

“The hardest part of treating malaria in a village is not the medicine. It is day three,” said Dr. Lurdes Macuácua, the trial’s principal investigator at the Manhiça Health Research Center, an hour north of the capital. Children feel better after the first doses, she said, and parents, often facing a long walk to a clinic, stop giving the pills. Surveys in the trial regions found that about a third of courses were not completed, which leaves surviving parasites and, over time, breeds resistance. “One dose, watched by the nurse, removes that problem entirely.”

Malaria killed an estimated 600,000 people in 2024, most of them children in sub-Saharan Africa, and Mozambique has among the highest burdens in the world, with about 10 million cases a year in a population of 34 million. The country’s malaria program has made progress with bed nets, indoor spraying and, since 2023, a vaccine for infants, but a resurgence of mosquitoes resistant to common insecticides has stalled gains in the north.

Ana Paula Sitoe, whose 4-year-old son was enrolled in the trial after a fever in March, said she had treated him for malaria four times before. “Every time I would forget a dose, or he would spit it out, or we would run out,” she said. “This time the nurse gave him one tablet and we went home. That was it.”

The result’s promise is also its danger. A single-dose drug that is given widely could, if parasites develop resistance to it, lose its usefulness quickly, and some experts urged that ganaquine be deployed only in combination with a partner drug. “A new mechanism is the most valuable thing we have had in malaria since artemisinin, and we should not spend it alone,” said Dr. Samuel Nkosi, a malaria adviser to the World Health Organization’s regional office in Brazzaville, who attended the presentation. “The question for regulators is whether they approve the drug that works today or the combination that will still work in 2040.”

The partnership said it would submit the single-agent results to regulators in the three trial countries and to the W.H.O. for prequalification by early next year, and that a trial of ganaquine paired with a second new compound would begin in 2027. The projected price is under $1 per treatment.

Dr. Macuácua said the trial had changed how parents in Manhiça talked about the disease. “They ask for the one-pill medicine by name,” she said. “We have to tell them it is not here yet. But it is coming, and for once I believe it.”