The COVID-19 pandemic has affected the way of teaching and learning in medicine. Conventional medical education has been fully transformed to open distance learning that includes the full utilization of various digital platforms. Thus, this study explored the impact of digital learning usage on learning motivation among medical students of Universiti Kebangsaan Malaysia (UKM) before and during the COVID-19 pandemic period. A validated Students Motivation towards Science Learning (SMTSL) tool was used to assess the learning motivation of UKM undergraduate medical students throughout years 1 to 5. Digital learning during the COVID-19 pandemic was significantly higher compared to before the pandemic (p < 0.05) but there was no significant difference (p = 0.872) in learning motivation. The use of digital learning among clinical students was significantly higher during the COVID-19 pandemic as compared to preclinical students (p < 0.05). There was a moderately strong correlation (r = 0.512) between digital learning and learning motivation. Hence, digital learning should be utilized as an additional driving factor to increase learning motivation, especially during this current pandemic.