We conducted a cluster randomized trial comparing the target population and timing of mass drug administration (MDA) with praziquantel for control of schistosomiasis in villages in western Kenya with high initial prevalence (> 25%) according to a harmonized protocol developed by the Schistosomiasis Consortium for Operational Research and Evaluation. A total of 150 villages were randomized into six treatment arms (25 villages per arm), were assessed at baseline, and received two or four rounds of MDA using community-wide (CWT) or school-based (SBT) treatment over 4 years. In the fifth year, a final evaluation was conducted. The primary outcomes were prevalence and intensity of Schistosoma mansoni infections in children aged 9-12 years, each year their village received MDA. Baseline and year 5 assessments of first-year students and adults were also performed. Using Poisson and negative binomial regression with generalized estimating equations, we found similar effects of CWT and SBT MDA treatment strategies in children aged 9-12 years: significant reductions of prevalence of infection in all arms and of heavy-intensity (≥ 400 eggs/gram) infections in most arms but no significant differences between arms. Combined arms of villages that received four rounds of treatment had greater reduction than villages in arms that only received two rounds of treatment. Surprisingly, we also found benefits of SBT for first-year primary students and adults, who never received treatment in those arms. Our data support the use of annual SBT for control programs when coupled with attention to infections in younger children and occasional treatment of adults.