Purpose: Poor sleep quality is common in medical students and is associated with a number of negative health outcomes. However, the prevalence estimates of poor sleep quality in medical students vary widely across studies. We thus conducted a meta-analysis of the prevalence of poor sleep quality and its mediating factors in medical students. Methods: A systematic literature search of PubMed, EMBASE, Web of Science, PsycINFO, and Medline Complete was performed. The random-effects model was used to analyze the pooled prevalence of poor sleep quality and its 95% confidence intervals (CIs). Results: A total of 57 studies with 25,735 medical students were included. The pooled prevalence of poor sleep quality was 52.7% (95% CI: 45.3% to 60.1%) using the Pittsburgh Sleep Quality Index (PSQI). The pooled mean total PSQI score across 41 studies with available data was 6.1 (95% CI: 5.6 to 6.5). Subgroup analyses found that PSQI cutoff value and study region were associated with the prevalence of poor sleep quality (P = 0.0003 VS. P = 0.005). Across the continents, poor sleep quality was most common in Europe, followed by the Americas, Africa, Asia, and Oceania. Meta-regression analyses found that smaller sample size (slope = − 0.0001, P = 0.009) was significantly associated with higher prevalence of poor sleep quality. Conclusions: Poor sleep quality is common among medical students, especially in Europe and the Americas continets. Due to the negative health outcomes, regular screening of poor sleep quality and effective interventions are needed for medical students.