Background: Suicidal ideation (SI) and suicide planning (SP) are associated with an increased risk of future suicide. We performed a meta-analysis of observational studies to estimate the prevalence of SI and SP in patients with major depressive disorder (MDD) and its associated factors. Methods: A systematic literature search was conducted in PubMed, EMBASE, PsycINFO and Web of Science from their commencement date until 7 October 2020. Original studies containing data on the prevalence of SI and SP in individuals with MDD were analyzed. Results: Forty-six articles covering 53,598 patients were included in the meta-analysis. The overall prevalence of SI was 37.7% (95% confidence interval (CI): 32.3–43.4%) and the pooled prevalence of SP was 15.1% (95% CI: 8.0-–26.8%). Subgroup analyses revealed that the timeframe over which SI was assessed, source of patients, study design, and diagnostic criteria were significantly associated with the pooled prevalence of SI. Meta-regression analyses revealed that the Hamilton Depression Rating Scale (HAMD) score and percentage of male participants were positively associated with the pooled prevalence of SI. Study quality and mean age were negatively associated with the pooled prevalence of SI. In contrast, survey year and study quality were negatively associated with pooled prevalence of SP Limitation: SI and SP were self-reported and subject to recall bias and impression management. Conclusions: SI and SP are common in patients with MDD, especially among inpatients. Preventive measures and treatments focusing on factors associated with SI and SP may reduce the risk of suicide in patients with MDD.