University administrators and mental health clinicians have raised concerns about depression and anxiety among Ph.D. students, yet no study has systematically synthesized the available evidence in this area. After searching the literature for studies reporting on depression, anxiety, and/or suicidal ideation among Ph.D. students, we included 32 articles. Among 16 studies reporting the prevalence of clinically significant symptoms of depression across 23,469 Ph.D. students, the pooled estimate of the proportion of students with depression was 0.24 (95% confidence interval [CI], 0.18–0.31; I2 = 98.75%). In a meta-analysis of the nine studies reporting the prevalence of clinically significant symptoms of anxiety across 15,626 students, the estimated proportion of students with anxiety was 0.17 (95% CI, 0.12–0.23; I2 = 98.05%). We conclude that depression and anxiety are highly prevalent among Ph.D. students. Data limitations precluded our ability to obtain a pooled estimate of suicidal ideation prevalence. Programs that systematically monitor and promote the mental health of Ph.D. students are urgently needed.