Background Schistosomiasis is a neglected tropical disease that continues to cause morbidity and mortality in Sub Saharan Africa. Due to its endemicity, co-infection with malaria is common. The diseases cause anaemia and impaired nutritional status among children. We investigated the prevalence of intestinal schistosomiasis and its association with malaria, anaemia and nutritional status among school children. Methods This was a cross sectional survey among 830 children in Nyamikoma village along Lake Victoria in Tanzania. A pre-tested questionnaire was used to collect socio-demographic data, history of drug use, and clinical data. Two faecal samples were collected on two consecutive days and analyzed using thick smears Kato Katz method. Diagnosis of malaria was done by malaria rapid diagnostic test, and haemoglobin concentration was determined using Hemo-Cue. Nutritional status was assessed by anthropometric measurements. Results The overall prevalence of intestinal schistosomiasis was 90.6% (95% CI = 88.6%-92.6%). Intensity of infection was light 24.1% (200/830), moderate 38.4% (319/830) and heavy 28.1% (233/830). Pre-adolescents (�12 years) were more infected with intestinal schistosomiasis (93.2%) than adolescents (>12 years) (84.7%) (p < 0.001). Prevalence of malaria was 1.7% (14/824), and that of intestinal schistosomiasis-malaria co-infection was 1.6% (13/824). The overall prevalence of anaemia was 24.6% (95%CI = 18.7%-30.5%). Severe anaemia was found in 2.3% (19/824) of study participants. The prevalence of stunting and wasting were 29.0% and 11.3%, respectively. On both univariate and multivariate regression analysis, only lower age was significantly associated intestinal schistosomiasis