To evaluate the effect of exercise programs on reduction of musculoskeletal injury (MSI) risk in military populations. Systematic review and meta-analysis. A database search was conducted in PubMed/MEDLINE, EMBASE, Cochrane Library, CINAHL, SPORTdiscus, WHO International Clinical Trials Registry Platform Search Portal, Open Gray, National Technical Reports Library, and reference lists of included articles up to July 2019. Randomized and cluster-randomized controlled trials evaluating exercise programs as preventive interventions for MSIs in armed forces compared to other exercise programs or to usual practice were eligible for inclusion. Two authors independently assessed risk of bias and extracted data. Data were adjusted for clustering if necessary and pooled using the random-effects model when appropriate. We included 15 trials in this review, with a total number of 14 370 participants. None of the included trials appeared to be free of any risk of bias. Meta-analysis and Grading of Recommendations, Assessment, Development and Evaluations (GRADE) assessment could be performed for static stretching compared to no stretching (3532 participants), showing low quality of evidence indicating no favorable effect of stretching. Gait retraining, an anterior knee-pain targeted program, and resistance exercises showed cautious favorable effects on reducing injury risk in military personnel. The current evidence base for exercise-based MSI prevention strategies in the military is of low quality. Areas worthy of further exploration include the effects of gait retraining, anterior knee-pain targeted programs, agility training, and resistance training programs, on medial tibial stress syndrome incidence, anterior knee pain incidence, attrition due to injuries and any type of MSI, respectively.