Background Neglected tropical diseases, such as soil-transmitted helminths and Schistosomiasis, are prevalent in sub-Saharan Africa, particularly Ogun State, Nigeria. School-based mass drug administration program is the primary control intervention, but the coverage and uptake of this intervention have been inadequate. This study aimed to investigate community perceptions of school-based mass drug administration programs for these infections in Ogun State, Nigeria, and identify the barriers to their uptake and coverage. Methodology/Principal findings The study used a qualitative research approach involving focus group discussions and in-depth interviews with community members and stakeholders engaged in neglected tropical disease control programs in Ogun State, Nigeria. A semi-structured questionnaire guided the exploration of ideas, and the data were analyzed using the QRS Nvivo 12 software package. The study found several barriers, such as the influence of parents, lack of sufficient knowledge, and side effects. The study recommended strategies such as improving community sensitization and engagement, drug distribution and performance, and enhancing partner collaboration and coordination to improve the school-based mass drug administration programs. Conclusions/Significance The study revealed correct perceptions of transmission but some misconceptions about disease causation, transmission, and drug safety. Participants expressed a desire for better sensitization campaigns and more assurances of their safety. The study recommends strengthening health education messages and increasing the visibility of on-site medical personnel. The findings have implications for improving the performance of these programs and reducing the burden of intestinal parasitic infections in the community. The study highlights the need for community engagement and education, health system support, and partner collaboration to successfully implement mass drug administration programs.