This paper presents a first attempt at modelling the possible cost and effectiveness of reaching non-enrolled children through school-based programmes using empirical data from Egypt. A sex/school-attendance/age-structured population dynamic model was used to predict trends in infection and early disease. Four treatment delivery strategies were compared: school-based (coverage of 85%) and school-aged targeted (coverage of 25, 50 and 85%). The school-aged targeted strategies also included the school-based programme. For each alternative strategy, the maximum unit cost was calculated to obtain a cost-effectiveness ratio equal or smaller to the one obtained with the school-based programme (unit cost of US$ 0·60). The analysis showed that, for S. mansoni in Lower Egypt, a programme where only 85% of children attending school were treated would still prevent 77% of the early disease cases prevented with a programme where 85% of all school-age children were treated. However, using the school-aged targeted strategy, from US$ 0·06 to US$ 1·03 extra unit costs could be spent to reach non-enrolled children and still be more cost-effective. Treating non-enrolled children is an important consideration in maximizing the effectiveness of treatment programmes while maintaining a cost-effectiveness comparable to school-based delivery.