Evidence on the cost of acute malnutrition treatment, particularly with regards to simplified approaches, is limited. The objective of this study was to determine the cost of acute malnutrition treatment and how it is influenced by treatment protocol and programme size. We conducted a costing study in Kabléwa and N’Guigmi, Diffa region, where children with acute malnutrition aged 6–59 months were treated either with a standard or simplified protocol, respectively. Cost data were collected from accountancy records and through key informant interviews. Programme data were extracted from health centre records. In Kabléwa, where 355 children were treated, the cost per child treated was USD 187.3 (95% CI: USD 171.4; USD 203.2). In N’Guigmi, where 889 children were treated, the cost per child treated was USD 110.2 (95% CI: USD 100.0; USD 120.3). Treatment of moderate acute malnutrition was cheaper than treatment of severe acute malnutrition. In a modelled scenario sensitivity analysis with an equal number of children in both areas, the difference in costs between the two locations was reduced from USD 77 to USD 11. Our study highlighted the significant impact of programme size and coverage on treatment costs, that cost can differ significantly between neighbouring locations, and that it can be reduced by using a simplified protocol.