The Ugandan national control programme for schistosomiasis has no clear policy for inclusion of preschool-children (≤5 years old) children. To re-balance this health inequality, we sought to identify best diagnosis of intestinal schistosomiasis, observe treatment safety and efficacy of praziquantel (PZQ), and extend the current WHO dose pole for chemotherapy. We examined and treated 363 preschool children from shoreline villages of Lakes Albert and Victoria, and found that 62·3% (CI95 57·1–67·3) of the children were confirmed to have intestinal schistosomiasis. One day after treatment, children were reported as having headaches (3·6%), vomiting (9·4%), diarrhoea (10·9%) and urticaria/rash (8·9%) with amelioration at 21-day follow-up, where the parasitological cure rate was found to be 100·0%. Height and weight data were collected from a further 3303 preschool children to establish and validate an extended PZQ dose pole that now includes two new height-intervals: 60–84 cm for one-half tablet and 84–99 cm for three-quarter tablet divisions; which would result in 97·6% of children receiving an acceptable dose (30–60 mg/kg). To conclude, preschool children in lakeshore communities of Uganda are at significant risk of intestinal schistosomiasis; we now strongly advocate for their immediate inclusion within the national control programme to eliminate this health inequity.