A mathematical model, based on a deterministic differential equation framework, has been developed to predict the impact of community chemotherapy programmes for human schistosomiasis. Here, this model is validated using data collected from a long-term control programme for urinary schistosomiasis on the island of Pemba, Zanzibar, United Republic of Tanzania, initiated in 1986 and still ongoing, in which schoolchildren were offered praziquantel chemotherapy every 6 months. Prevalence of infection and blood in urine were monitored in all the schools (total 26000 children from 60 schools) and more detailed data were collected in selected evaluation schools. Model predictions were run by using the initial prevalence as input. The predictions were very close to the observed decreases in prevalence and in prevalence of blood in urine. The correspondence improved further when the data were combined, going from single school level to district, and when the entire data set was combined. The accuracy of the predictions suggests that this model could be used as a tool to predict the consequences of chemotherapy control programmes. It is currently in press as a Windows software package under the name of ‘EpiSchisto’.