Soil-transmitted helminthiasis (STH) and schistosomiasis (SCH) are among the most prevalent neglected tropical diseases (NTDs), affecting 1.5 billion globally, with a significant burden in sub-Saharan Africa, particularly Nigeria. These diseases impair health and contribute to socio-economic challenges, especially in children, undermining educational and future economic prospects. The 2030 NTD Roadmap highlights Mass Drug Administration (MDA) as a critical strategy for controlling these NTDs, targeting vulnerable populations like school-age children. Despite some successes, challenges persist, indicating the need for deeper insights into program implementation. This study focuses on the perspectives of health workers implementing MDA in selected local government areas (LGAs) of Ogun State, Nigeria, aiming to identify challenges and enablers that align with the broader NTD 2030 goals. 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, between July and September 2022. 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. 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.