The temporary closure of learning institutions during the COVID-19 pandemic has dramatically reduced the physical activity of students across all ages. Therefore, this study aimed to investigate the prevalence of physical inactivity and the patterns of physical activity among university students in confinement. This cross-sectional study involved 147 Malaysian students and 107 Indonesian students. Body weight before the pandemic and during the pandemic was self-reported by the respondents, and the International Physical Activity Questionnaire-Short Form (IPAQ-SF) was used to assess the physical activity and sedentary behavior of the respondents. The findings revealed that 79.6% of Malaysians and 77.6% of Indonesians were physically active during the confinement. There was no significant difference ( < 0.05) in the duration devoted to vigorous-intensity activity (M = 0.00 MET minutes/week and M = 480.00 MET minutes/week) and moderate-intensity activity (M = 0.00 MET minutes/week and M = 0.00 MET minutes/week) among the studied population. During the pandemic, Malaysian students (M = 1386.00 MET minutes/week) devoted a significantly higher duration to walking (M = 1386.00 MET minutes/week) and sedentary behavior (9.16 ± 4.47 h/day) than Indonesian students (M = 990.00 MET minutes/week and sedentary behavior = 7.85 ± 4.27 h/day). Overall, no significant difference was noted in the total physical activity of Malaysian and Indonesian students during the pandemic (M = 2826.00 MET minutes/week and M = 1782.00 MET minutes/week). Findings from Spearman's rank correlation test suggested that there was a weak inverse correlation between the duration engaged in vigorous-intensity activity and weight change among the Malaysian students (r = -0.199, = 0.016), after adjusting for gender and age. Overall, the closure of learning institutions and exercise facilities has further prevented individuals from complying with the WHO recommendation of moderate-to-vigorous physical activity during the period of home confinement.