Around half of the population of Afghanistan resides in areas at risk of malaria transmission. Two species of malaria (Plasmodium vivax and Plasmodium falciparum) account for a high burden of disease—in 2011, there were more than 300,000 confirmed cases. Around 80–95% of malaria is P. vivax. Transmission is seasonal and focal, below 2,000 m in altitude, and in irrigated areas which allow breeding of anopheline mosquito vectors. Malaria risk is stratified to improve targeting of interventions. Sixty-three of 400 districts account for ∼85% of cases, and are the target of more intense control efforts. Pressure on the disease is maintained through case management, surveillance, and use of long-lasting insecticide-treated nets. Plasmodium vivax treatment is hampered by the inability to safely treat latent hypnozoites with primaquine because G6PD deficiency affects up to 10% of males in some ethnic groups. The risk of vivax malaria recurrence (which may be as a result of reinfection or relapse) is around 30–45% in groups not treated with primaquine but 3–20% in those given 14-day or 8-week courses of primaquine. Greater access to G6PD testing and radical treatment would reduce the number of incident cases, reduce the infectious reservoir in the population, and has the potential to reduce transmission as a result. Alongside the lack of G6PD testing, under-resourcing and poor security hamper the control of malaria. Recent gains in reducing the burden of disease are fragile and at risk of reversal if pressure on the disease is not maintained.