Modular learning was used to assist elementary learners in continuing their education during the pandemic. This modular learning posed academic challenges. This phenomenological study delved into the academic challenges of modular learning of public-school elementary school learners. Validated In-depth interview protocol (IDI) was used to collect the data from ten (10) Grade six learners. Findings revealed that these academic challenges include unfavorable learning environments, reading comprehension issues, lack of motivation, and poor quality of printed learning modules that affect the learners ability to comprehend and finish the module effectively. Consequently, modular learning allows learners to take responsibility for their learning by utilizing the available answers key, optimizing internet usage, scheduling time properly, and guessing answers. Considerably, the learners used face-to-face conversations, personal messages, and phone calls to communicate their educational queries. Moreover, the structure of self-learning modules facilitates independent study and complicates learners understanding. It is recommended that there is a need to enhance policies for improving module quality, allocate sufficient funds to improve the printed module quality, conduct relevant teacher training and workshops for developing quality printed modules, and sustain the home visitation program to monitor students modular learning progress.