Background: Mass Drug Administration (MDA) Programs has been conducting bi-annually at school level to eliminate Soil Transmitted Helminthiasis (STH) from Bangladesh since 2008. Because of very low MDA coverage in Bangladesh, this study explored the perceptions of stakeholders about MDA program implementation, knowledge of students regarding helminthiasis and MDA including its potential barriers. Methods: 258 students of grade IV of three public schools from Khulna district, Bangladesh were randomly selected. This study follows mixed-method approach while Qualitative methods were used to evaluate the perception, barriers and favourable environment based on IDIs and FGDs with key stakeholders and quantitative method used to assess the students’ response to School-Based Health Education (SBHE) intervention and knowledge of STH and MDA. Results: In result, positive understanding and attitude towards MDA program are seen within community as well as have basic knowledge on STH. Rumour of drugs potential side effects and insufficiently trained manpower are found as key barriers. After SBHE intervention among urban and rural students’ knowledge improved by 64.31% and 13.04% respectively including MDA coverage has increased by 40.08% and 8.69% respectively as well. Conclusions: SBHE intervention improves knowledge, but to make that knowledge effective and sustainable, teachers need to get proper trainings on regular basis. Improved knowledge of the community can increase MDA coverage if we are able to remove the program obstacle like rumours of side effect of the medicine and constraints of skilled human resources.