Prevalence of schistosomiasis in Ezperanza, Agusan del Sur, continued to significantly increase in 2018 but the Mass Drug Administration (MDA) Coverage decreased in the same year. This notable problem on the prevalence of the disease inspite of government efforts exposes a critical gap between the goals and the implementation of MDA as a public health program. This study investigates several factors that lead to the downfall of MDA coverage in the said municipality. Descriptive mixed-method approach was used. A total of 390 household heads were surveyed and 20 of which were subjected to Focus Group Discussions (FGD). Further, 30 health workers and 13 barangay officials have undergone FGD to deeply understand the gaps and challenges that hinder the implementation of MDA in the community.  Results showed that community’s knowledge and participation to the program are poor. Barangay officials are not strongly involved in the MDA program inspite of their vital role. Experiences revealed that adverse reactions to drugs were due to the fact that people took the medicine with empty stomachs. Major findings of the study have resulted to the proposed institutionalization of MDA program at the Barangay level.