Education actively helps us develop our well-being and health, but postgraduate students are at high risk of depression. The prevalence of depression symptoms varies from 6.2% to 84.7% among them, and its changes throughout the years remains unclear. The present study aimed to estimate the real prevalence of depression symptoms among postgraduate students and the changes from 1980 to 2020. Thirty-seven primary studies with 41 independent reports were included in the meta-analysis (none reports were in high-quality, three were medium-to-high quality, 20 were low-to-medium quality, and 18 were low-quality), involving 27,717 postgraduate students. The pooled prevalence of overall, mild, moderate, and severe depression symptoms was 34% (95% CI: 28–40, I2 = 98.6%), 27% (95% CI: 22–32, I2 = 85.8%), 13% (95% CI: 8–21, I2 = 97.3%), and 8% (95% CI: 6–11, I2 = 81.0%), respectively. Overall, the prevalence of depression symptoms remained relatively constant through the years following 1980 (overall: β = −0.12, 95% CI: [−0.39, 0.15], p = 0.39; mild: β = 0.24, 95% CI: [−0.02, 0.51], p = 0.07; moderate: β = −0.24, 95% CI: [−0.75, 0.26], p = 0.34; severe: β = 0.13, 95% CI: [−0.25, 0.51], p = 0.50). Doctoral students experienced more depressive symptoms than did master's students (43% vs. 27%; Q = 2.23, df = 1, p = 0.13), and studies utilising non-random sampling methods reported a higher prevalence of mild depression and lower moderate depression symptoms than those that used random sampling (overall: 34% vs. 29%; Q = 0.45, df = 1, p = 0.50; mild: 29% vs. 21%; Q = 1.69, df = 1, p = 0.19; moderate: 16% vs. 25%; Q = 1.79, df = 1, p = 0.18; severe: 8% vs. 9%; Q = 0.13, df = 1, p = 0.72) despite these differences was not statistically significant. The prevalence of depression symptoms was moderated by the measurements and the quality of primary studies. More than one-third of postgraduates reported depression symptoms, which indicates the susceptibility to mental health risk among postgraduates. School administrators, teachers, and students should take joint actions to prevent mental disorders of postgraduates from increasing in severity.