Time management (TM) is a crucial academic ability, especially as schools transition from conventional to virtual instruction delivery during the coronavirus disease 2019 (COVID-19) pandemic. The aim of the study was to identify the variables affecting medical science undergraduate students in Iran during the COVID-19 pandemic. This web-based cross-sectional study was conducted in 2021. Participants included medical students and students pursuing a bachelor’s degree in medical sciences. They were conveniently selected from medical universities across Iran. A demographic questionnaire and the Trueman and Hartley Time Management Questionnaire were used as study instruments. Telegram and WhatsApp were used for data collection and sampling. The SPSS program (version 22.0) and multiple linear regression (MLR) analysis were used to analyse the data. In total, 1,183 students completed the questionnaires in their entirety. The mean of their age was 22.08±3.15 years and the majority of them were female (62.04%). The mean TM score was 45.19±8.3 (with a range of 14–70), and gender, grade point average (GPA), daily study time, daily internet use time, work status, and kind of university were the significant predictors of TM ability (p < 0.05). Iranian students have a moderate level of TM skill, and their work status, GPA, daily study time, daily Internet usage, and type of university are the main predictors of their TM. The shift from traditional to virtual learning during the COVID-19 pandemic highlights the importance of equipping medical students with necessary TM skills.