Background: The unprecedented COVID-19 pandemic has resulted in social distancing and isolation which leads to insufficient physical activity and thereby increases sedentary behaviors. Hence, this study aimed to assess the prevalence of insufficient physical activity and sedentary behaviors among medical students during the COVID-19 lockdown in Pakistan, and to determine their associated factors. Methods: A cross-sectional online survey was carried out among 407 medical students from the Punjab and Sindh provinces between May and June 2020. To collect data, an e-questionnaire was sent to obtain informed consent along with questions concerning socio-demographics as well as an International Physical Activity Questionnaires–Short Form (IPAQ–SF). Results: As per the IPAQ, almost five in ten participants were physically inactive (48.2%), and 45.2% reported sedentary behaviors. Participants with insufficient physical activity were more likely to report sedentary behaviors than their counterparts (AOR = 2.53; 95% CI = 1.66–3.85, p < 0.001). The odds of insufficient physical activity were higher among the participants who did not strictly follow the COVID-19 preventive measures (AOR = 2.51; 95% CI = 1.35–4.69, p = 0.004); similarly, there were increased odds of sedentary behaviors observed among participants within a normal weight range compared to those who were underweight (AOR = 2.69; 95% CI = 1.76–4.11, p < 0.001). Conclusions: Insufficient physical activity and sedentary behavior are prevalent among medical students in Pakistan during the COVID-19 pandemic. These findings indicate the importance of establishing tailored policies and programs to encourage young adults to engage in physical activity.