Soil-transmitted helminths and <i>Schistosoma haematobium</i> affect more than 3 billion people globally and mainly occur in sub-Saharan Africa. The present study assessed the overall infection status of a 1716-student cohort of school-children in Zanzibar and applied mass drug administration (MDA) to the cohort from 2007 to 2009. Schools in Pemba, Zanzibar, had a much higher prevalence of soil-transmitted helminth infections than those in Unguja, and the Chaani, Ghana, and Machui schools of Unguja exhibited high <i>S. haematobium</i> infection rates. The MDA program only partially controlled parasite infections, owing to high rates of re-infection. The infection rate of <i>S. haematobium</i> across all 10 schools, for example, was only reduced by 1.8%, and even this change not significant, even though the <i>S. haematobium</i>infection rates of the Chaani and Mzambarauni schools were significantly reduced from 64.4 and 23.4%, respectively, at the first screening, to 7.3 and 2.3% at the last screening. The overall infection rate of <i>Ascaris lumbricoides</i> was reduced from 36.0% at the first screening to 22.6% at the last screening. However, the infection rates for both <i>Trichuris trichiura</i>and hookworm were generally unaffected by MDA. In the future, parasite control programs should involve strategically designed MDA schedules and holistic intervention (e.g., sanitation improvement, hygiene behavior changes, and control of intermediated hosts).