Worldwide, millions of children are affected by armed conflict. However, data on the prevalence of mental disorders among these children is sparse. We aimed to determine the prevalence of mental disorders among children affected by war using a systematic review and meta-regression analysis. We systematically reviewed existing literature to identify studies on prevalence of post-traumatic stress disorder (PTSD), anxiety, depression and psychosis among children exposed to armed conflict. We searched electronic databases and references listed in studies to obtain eligible studies. We pooled studies using the random-effects method and explored heterogeneity using meta-regression analysis. Seventeen studies met our inclusion criteria. Studies included 7,920 children. Sample sizes ranged from 22 to 2,976. Four studies were conducted during a conflict and others during post-conflict. All the studies reported PTSD as the primary outcome ranging from 4.5 to 89.3%, with an overall pooled estimate of 47% (9% CI: 35-60%, I2 = 98%). Meta-analysis heterogeneity was attributable to study location (OR 1.33, 95% CI: 1.27-1.41), method of measurement (OR 1.36, 95% CI: 1.29-1.44) and duration since exposure to war (coefficient 0.17, 95% CI: 0.94-0.25). In addition, four studies reported elevated depression that allowed pooling (43%, 95% CI: 31-55%) and three studies reported elevated anxiety disorders allowing pooling (27%, 95% CI: 21-33%). Our systematic review suggests a higher prevalence rate of mental disorders among children exposed to conflict than among the general population. Given the number of current conflicts, there is a paucity of information regarding mental disorders among children affected by war.