In areas where HIV and intestinal schistosomiasis are highly endemic, co-infections of the two diseases in a single human host are frequent. Evidence in adult populations indicates that HIV and intestinal schistosomiasis are associated with negative health impacts. However, the topic of HIV and schistosomiasis in paediatric populations has received little attention. The present study determined the prevalence and intensity of Schistosoma mansoni infection in a paediatric population on antiretroviral therapy (ART) in north-western Tanzania. A cross-sectional study was conducted among HIV-infected children aged 1-16 years on ART attending a Care and Treatment Clinic at Ukerewe Designated District Hospital, north-western Tanzania. Single stool and urine samples were collected and screened for S. mansoni eggs and circulating cathodic antigen (CCA), using the Kato-Katz (KK) technique and point-of-care CCA (POC-CCA) rapid urine test, respectively. A total of 134 children with a median age of 10 years (IQR 7-12 years) participated in the study. Of these, 44.8% (60/134) and 55.2% (74/134) were female and male, respectively. The overall prevalence of S. mansoni based on the KK technique and POC-CCA rapid test were 10.7% (95% CI 5.9% to 18.4%) and 33.8% (95% CI 26.2% to 42.4%), respectively. The overall geometrical mean eggs per gram of faeces was 293.9 GM-epg (95% CI 123.3 to 700.9). A small proportion of the children had moderate (4.9%, 5/103) and heavy (3.8%, 4/103) intensity of infection. Paediatric populations on ART are co-infected with S. mansoni infection. Screening and treatment of intestinal schistosomiasis at initiation of ART is recommended to reduce the risk of developing hepatosplenic disease, schistosomiasis-related immune reconstitution inflammatory syndrome and the possible adverse effect of schistosomiasis on outcome of ART.