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Introduction: The Faculty of Medicine, University of Moratuwa, established during the COVID-19 pandemic, was compelled to conduct the teaching activities online for the first intake of students until their first bar examination. Online learning is known to be linked to several health issues. This study aims to explore the academic performance and perceived health effects related to online learning in the Faculty of Medicine, Moratuwa. Methods: A descriptive cross-sectional study was conducted among all 104 first-intake students using an anonymous online self-administered questionnaire to explore health effects and academic performance after ethical clearance. Results: Out of 104 students, 82 students responded (response rate=78.85%). Majority participated from home using their own laptop (74.4%) and personal Wi-Fi (69.5%) and spent 5-10 hours daily for online academic activities (72%). Majority complained of related physical (86.6%), and psychological (81.7%) health issues: eye problems (69.5%), headache (47.6%), backache (43.9%), stress (46.3%) and concentration difficulties (45.1%). The first bar examination was cleared by 84.1% with the majority (52.4%) obtaining classes. There was a statistically significant positive association (p< .05) between physical and psychological health concerns with the average screen-time spent on academic activities, but not with the academic performance. There was also no statistically significant association between screen-time and academic performance. Conclusions: Majority of students using online learning had related physical and psychological health issues which were positively associated with the screen-time though not with academic performance. Designing online activities with less screen time may be considered as a strategy to minimise health effects related to online learning.