Background Neglected tropical diseases, such as soil-transmitted helminths and schistosomiasis, are prevalent in sub-Saharan Africa, particularly in Nigeria. Mass drug administration is the primary control intervention, but the coverage and utilization of these programs are often inadequate. This study aimed to investigate community perceptions of school-based mass drug administration programs for these infections in Nigeria and to identify the barriers to their utilization and coverage. Methodology/Principal Findings The study used a qualitative research approach, involving focus group discussions and in-depth interviews with stakeholders involved in neglected tropical disease control programs in Ogun State, Nigeria. A semi-structured questionnaire was used to guide the exploration of ideas, and the data were analyzed using the QRS Nvivo 12 software package. The study found several barriers such as poor drug acceptability, accessibility, and effectiveness, low knowledge and awareness of the diseases and control interventions, inadequate community engagement and involvement, and weak health system and partner support to the utilization and coverage of control interventions for soil-transmitted helminths and schistosomiasis. The study also identified recommendations for addressing these barriers, including community sensitization and engagement, improving drug distribution and effectiveness, strengthening health system support, and enhancing partner collaboration and coordination. 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. To improve mass drug administration programs, the study recommends strengthening health education messages and increasing the visibility of on-site medical personnel. The findings have implications for improving the effectiveness 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 ensure the successful implementation of mass drug administration programs.