Most of what students learn is acquired in school. However, some pupils encounter learning difficulties which are not properly addressed by the teachers. This study aims to identify and examine the factors affecting the academic performance of ten (10) Grade Five pupils in Leyte Normal University-Integrated Laboratory School. The study used qualitative single-case study design, and participants were selected through purposive sampling. The top five (5) pupils in the high performing group and five (5) pupils in the low performing group were selected in that process. Data was collected using semi-structured interviews and direct observation of the participants. As a result, six major themes were derived from the findings after data analysis was conducted, namely: Self-Driven Activities in Learning, Challenges in Learning, Styles in Learning, References used in Learning, Scaffolds in Learning and Coping Mechanisms in Learning. This study could provide ways and awareness to all stakeholders in education on how to improve pupils’ academic performance in school.