Schistosomiasis control programs are designed to reduce morbidity by providing mass drug administration (MDA) of praziquantel to at-risk populations. We compared morbidity markers between two cohorts of Kenyan schoolchildren that initially had high prevalence of Schistosoma mansoni infections. One cohort (N = 416 at year 1) received four rounds of annual MDA in a community-wide treatment (CWT) strategy. The other cohort (N = 386 at year 1) received school-based treatment (SBT) every other year over the 4-year period. We measured infection with S. mansoni and soil-transmitted helminths (STH) as well as subtle morbidity markers at year 1, year 3, and year 5 and compared cohorts with mixed models after controlling for age and gender. At year 5, neither overall S. mansoni prevalence nor the prevalence of high infection-intensity S. mansoni infection was significantly reduced compared with baseline in either the CWT cohort (N = 277 remaining) or the SBT cohort (N = 235 remaining). Nevertheless, by year 5, children in both cohorts demonstrated significant decreases in wasting, ultrasound-detected organomegaly, and STH infection along with significantly improved pediatric quality-of-life scores compared with year 1. Stunting did not change over time, but children who were S. mansoni egg-positive at year 5 had significantly more stunting than children without schistosomiasis. The only significant difference between arms at year 5 was a lower prevalence of STH infections in the CWT group.