We evaluated the effect of a local government unit-led, school-based, teacher-assisted mass drug administration (MDA) treatment of soil-transmitted helminthiasis (STH) on the morbidity of school children in selected provinces of western Visayas, the Philippines. Parasitological assessment was done on stool samples using the Kato-Katz technique. Nutritional status and school performance were also evaluated using secondary data from the Department of Education. The overall prevalence of STH decreased from 71.1% to 44.3% (p < 0.0001) and the prevalence of heavy infection with STH decreased from 40.5% to 14.5% (p < 0.0001), after two years of biannual MDA. The prevalence of underweight children decreased from 26.2% to 17.8% (p < 0.0001) and the prevalence of stunted children decreased from 20.9% to 16.6% (p < 0.0001) after two years of biannual MDA. School performance improved on standardized testing from a mean percentage of 53.8% to 64.6%. Advocacy, social mobilization, strong local government support and intersectoral collaboration with other agencies probably contributed to the success of the program.