Within the period of the year 2020, institutions around the globe shut down their entrances to diminish the spread of the viral occurrence in the course of the pandemic. This physical closure prompted a quick transition to modular distance learning, which handed parents and guardians more responsibilities for their children's education. This study aimed to investigate the challenges in modular learning modality experienced by 10 parents of children with special needs in Molocaboc Island. Adhering with the qualitative method of research and phenomenological approach, a researcher-made semi-structured method of an in-depth interview composed of three parts was utilized in the conduct of this study. The obstacles that parents of special learners encountered while completing the modular distance learning of their learners were analyzed using thematic coding. The data revealed four (4) themes focusing on the challenges of parents in home learning support system, balancing parents’ duties and responsibilities, parents’ background, and accessibility with emerged sub-themes each. The results indicated parents struggles and challenges amidst modular learning modality. Parents described having difficulties with home learning support system, balancing responsibilities, parents’ background, and accessibility. The result of the study also showed opportunities seen by the respondents in two (2) themes directing on the opportunities of modular distance learning and building success from strengths. The results suggested some important implications and recommendations for the department, local government unit, educators, and parents. The implication of this study is the need for adequate preparation for the challenges that will be encountered on the island where they may be assigned and to equip them with proper measures to deal with unexpected situations. The results of the study were the basis for feedbacking for the crafting of action plan for intervention.