Introduction: Malaria remains a real problem of public health. Its hospital care generates important expenditures for affected households. The present study aimed to estimate direct and indirect costs of severe child malaria in reference hospitals in Kinshasa. Methodology: This prospective study included 1,350 children under 15 years of age suffering from severe malaria. The study was performed between 1 January and 30 November, 2011. Data were collected in nine reference hospitals. The studied parameters were direct pre-hospital costs, direct hospital costs, and indirect costs. Costs were assessed from the household point of view. Results: Median costs associated with the disease ranged from 114 USD in confessional hospitals to 173 USD in state hospitals and 308 USD in private hospitals. Direct pre-hospital median costs ranged between 3 and 11 USD. Direct hospital costs reached 72 USD in confessional hospitals, 139 USD in state hospitals, and 254 USD in private hospitals. Indirect costs ranged from 22 USD in state hospitals to 30 USD in confessional hospitals and 46 USD in private hospitals, regardless of the status of the accompanying parent or guardian. Factors explaining the variability of costs were the neurological form of malaria, indirect recourse to hospital, socioeconomic level, type of prescribing person, child's status upon leaving the hospital, and child's transfusion status. Conclusions: The care of severe child malaria appeared to be expensive in private and state hospitals. A state subsidy of health care and regulation of the private sector would contribute to the reduction of malaria's financial impact.