Shifting learning process due to COVID-19 has led to increased burnout prevalence among medical students. Thus, this study aimed to assess burnout prevalence and its associated factors among Indonesian medical students during the COVID-19 pandemic. An online cross-sectional study was carried out among medical students in Malang, Indonesia. Burnout was assessed using the Maslach Burnout Inventory-Student Survey tool. Pearson’s Chi-square was used to assess significant associations, and binary logistic regression was conducted to evaluate the relationships between the predictor variables and burnout. The difference of each subscale score was evaluated using an independent samplettest. This study analyzed 413 medical students with a mean age of 21.1 ± 1.4 years old. About 29.5% and 32.9% of students reported a high level of emotional exhaustion and depersonalization, respectively, resulting in 17.9% of burnout prevalence. Stage of study was the only sociodemographic factor independently associated with burnout prevalence (odds ratio = 0.180, 95% confidence interval = 0.079–0.410,p-values = 0.000). Preclinical students had significantly higher levels of emotional exhaustion (p-value = 0.004, d = 0.3) and depersonalization (p-value = 0.000, d = 1.1), and lower levels of personal accomplishment (p-value = 0.000, d = -0.5). Around one-sixth of the medical students experienced burnout during the COVID-19 pandemic, with preclinical students being more prone to have burnout. Future study with other adjusted confounding factors is needed to completely understand the issue and obtain immediate interventional strategies to reduce burnout among medical students.