Severe acute malnutrition (SAM) is a high-fatality condition that affected 13.7 million children under five years of age worldwide in 2022, with complicated cases requiring extensive inpatient stay with an accompanying caregiver. Our objective was to assess the costs of inpatient treatment for complicated SAM in children aged 6 to 59 months in Northern Senegal and identify cost predictors. We performed a retrospective cost analysis, including 140 children hospitalized from January to December 2020 in five SAM inpatient treatment facilities. We adopted a societal perspective, including direct medical and non-medical costs and indirect costs. We extracted patients' sociodemographic and clinical data from medical records and conducted semi-structured interviews with healthcare staff to capture information on time allocation and care management. A multivariable generalized linear model with gamma family and a log link was used to investigate the factors associated with direct costs. Costs are expressed in 2020 international USD using purchasing power parity. Mean length of stay was 5.3 (SD = 3.2) days and diarrhoea was the cause of the admission in 55.7% of cases. Mean total cost was USD 431.9 (SD = 203.9), with personnel being the largest cost item (33% of the total). Households' out-of-pocket expenses represented 45.3% of total costs and amounted to USD 195.6 (SD = 103.6). Costs were significantly associated with gender (20.3% lower in boys), diarrhoea (27% increase), anaemia (49.4% increase), inpatient death (44.9% decrease), and type of facility (26% higher in hospitals vs. health centre). Our study highlights the financial burden of complicated SAM in Senegal in particular for families. This underscores the need for tailored prevention and social policies to protect families from the disease's financial burden and improve treatment adherence, both in Senegal and similar contexts.