Background: Epidemiological studies of paediatric cancer incidence in Sudan are rare.Objectives: The aim of this study was to provide baseline information about the epidemiology of childhood cancers in patients treated at the National Cancer Institute (NCI) in Wad Medani, Sudan.Methods: We performed a retrospective health facility–based study of cancer incidence and patient characteristics of children who were treated at the NCI from January 1999 to December 2015. The changing patterns of cancers incidence during the study period were also recorded.Results: Of 15 387 new patients with cancer who were registered at the NCI during the study period, 1159 (7.5%) were children (younger than 15 years). The mean age of the paediatric patients was 7 years, with standard deviation of 5. Most of the patients (36%) were 10 to 15 years old, 33% were 0 to 4 years old and 31% were 5 to 10 years old. Among the study population, 60% were males and 40% were females. Approximately 76% of children lived in rural areas in Sudan. Leukaemias (29%) and lymphomas (26%) comprised 55% of all paediatric cancers. Central nervous system (CNS) tumours constituted 6% of all paediatric tumours, whereas non-CNS embryonal tumours (i.e. nephroblastoma, neuroblastoma, hepatoblastoma and retinoblastoma) accounted for 20%. The average number of cases per year increased from 42 in 1999–2005 to 75 in 2006–2010 and 106 in 2011–2015.Conclusion: The number of patients seeking treatment for childhood cancers has increased every year in central Sudan. Leukaemias and lymphomas constitute more than half of these cancers. A population-based cancer registry is needed to determine the true incidence of childhood cancers in Sudan.