Background: Repeated mass drug administration (MDA) of antihelminthics to at-risk populations is still the main strategy for the control of soil-transmitted helminth (STH) infections. However, MDA, as a stand-alone intervention, does not prevent reinfection. Accordingly, complementary measures to prevent STH reinfection, such as health education and improved sanitation, as part of an integrated control approach, are required to augment the effectiveness of MDA for optimal efficiency and sustainability. Objective: The aim of this study is to determine the impact and generalizability of a school-based health education package entitled The Magic Glasses for STH prevention in the Philippines. Methods: We conducted a cluster randomized controlled intervention trial, involving 2020 schoolchildren aged 9-10 years, in 40 schools in Laguna Province, Philippines, to evaluate the impact of the school-based health education package for the prevention of STHs. The trial was conducted over the course of 1 year (June 2016 to July 2017). A total of 20 schools were randomly assigned to the intervention arm, in which The Magic Glasses Philippines health education package was delivered with the standard health education activities endorsed by the Philippines Department of Health (DOH) and the Department of Education (DepEd). The other 20 schools comprised the control arm of the study, where the DOH/DepEd's standard health education activities were done. At baseline, parasitological assessments and a knowledge, attitude, and practice survey were carried out in all schools. In addition, height, weight, and hemoglobin levels were obtained from each child (after parental consent), and their school attendance and academic performance in English and mathematics were accessed from the school records. The baseline and 2 follow-up surveys were completed using the same study measurements and quality-control assessments. Results: Key results from this cluster randomized intervention trial will shed light on the impact that The Magic Glasses health education package will have against STH infections in schoolchildren in the province of Laguna, located on the Island of Luzon, in the Calabarzon Region of the Philippines. Conclusions: The results of the trial will be used to assess the generalizability of the impact of The Magic Glasses health education package in different epidemiological and cultural settings, providing evidence for translation of this health education package into public health policy and practice in the Asian region and beyond. Trial Registration: Australian New Zealand Clinical Trials Registry number ACTRN12616000508471; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368849. International Registered Report Identifier (IRRID): DERR1-10.2196/18419.