Background: Soil-transmitted helminths (STH) and schistosomiasis are widespread neglected tropical diseases (NTDs), impacting 1.5 billion individuals, primarily in resource-limited settings. With the highest schistosomiasis prevalence in sub-Saharan Africa, Nigeria treats 20 million annually. Mass Drug Administration (MDA) programs target vulnerable groups like school-age children to tackle these diseases. This study explores health worker perspectives on MDA implementation in Ogun's selected LGAs, pinpointing challenges and enablers. Health workers' insights enhance program effectiveness, aligning with NTD 2030 goals. Methodology/Principal Findings: The study used a qualitative research approach involving focus group discussions and in-depth interviews with health workers 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 that the school-based MDA control program's efficacy largely relies on strong collaborations and partnerships, particularly with educators, community heads, and other stakeholders. These alliances and strategic communication methods, like town announcements and media campaigns, have been pivotal in reaching communities. However, the program does grapple with hurdles such as parental misconceptions, limited funds, insufficient staffing, and misalignment with the Ministry of Education. It is recommended to boost funding, foster early stakeholder involvement, enhance mobilization techniques, and consider introducing a monitoring card system similar to immunization. Conclusions/Significance: The MDA Integrated Control Programs for STH and SCH in Ogun State schools demonstrate a holistic approach, integrating knowledge, collaboration, communication, and feedback. Health workers have shown commitment and adeptness in their roles. However, achieving maximum efficacy requires addressing critical barriers, such as parental misconceptions and funding challenges. Adopting the recommended strategies, including proactive communication, increased remuneration, and introducing a tracking system, can significantly enhance the program's reach and impact. The involvement of all stakeholders, from health workers to community leaders and parents, is essential for the program's sustainability and success.