Aim To estimate the pooled prevalence and incidence of depression and its common comorbid mental disorders in persons with a malarial infection and its neurological complications Method We will conduct a systematic review and meta-analysis of studies published between January 1, 1960 and January 1, 2020, reporting the prevalence or incidence of common mental disorders and the risks in people with malaria. We will search the following databases: PubMed (MEDLINE), Scopus, OVID (HEALTH STAR), OVID (MEDLINE) and Joana Briggs Institute EBF Database. No age, geographical location, study-design or language limits will be applied. If multiple languages were used to describe and publish the same data, the English version was selected. This protocol was developed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols guidelines. Three reviewers (MC, YP, YY) will independently screen citations, abstracts and will identify full-text articles for inclusion, extract data and appraise the quality and bias of included studies. Discrepancies will be resolved by consensus or consultation with a fourth researcher (AS). Risk of bias of included studies will be assessed by the Newcastle-Ottawa Quality Assessment Scale. The primary outcomes will be the overall prevalence or incidence of depression and common comorbid mental disorders (CCMDs) in persons with malaria. We will use the random-effects model with a logit transformation of proportions for the pooling of studies. We will assess the between-study heterogeneity using I2 statistics, and Cochrane’s Q statistic (significance level < 0.05). We will perform subgroup meta-analyses to investigate geographical differences in mental disorders and risks of different mental disorders. We will conduct a meta-regression analysis, using study level median age, race and gender proportions, the proportion of study population with malaria, and percentage of the study population with a diagnosis of common mental disorders. We will report absolute differences in the overall probability of common mental disorders. The Egger’s test and funnel plots will be used to assess publication bias.