To investigate the effect of FIFA injury prevention programmes in football (FIFA 11 and FIFA 11+). Systematic review and meta-analysis. Randomised controlled trials comparing the FIFA injury prevention programmes with a control (no or sham intervention) among football players. MEDLINE via PubMed, EMBASE via OVID, CINAHL via Ebsco, Web of Science, SportDiscus and Cochrane Central Register of Controlled Trials, from 2004 to 14 March 2016. 6 cluster-randomised controlled trials had assessed the effect of FIFA injury prevention programmes compared with controls on the overall football injury incidence in recreational/subelite football. These studies included 2 specific exercise-based injury prevention programmes: FIFA 11 (2 studies) and FIFA 11+ (4 studies). The primary analysis showed a reduction in the overall injury risk ratio of 0.75 (95% CI 0.57 to 0.98), p=0.04, in favour of the FIFA injury prevention programmes. Secondary analyses revealed that when pooling the 4 studies applying the FIFA 11+ prevention programme, a reduction in the overall injury risk ratio (incidence rate ratio (IRR) 0.61; 95% CI 0.48 to 0.77, p<0.001) was present in favour of the FIFA 11+ prevention programme. No reduction was present when pooling the 2 studies including the FIFA 11 prevention programme (IRR 0.99; 95% CI 0.80 to 1.23, p=0.940). An injury-preventing effect of the FIFA injury prevention programmes compared with controls was shown in football. This effect was induced by the FIFA 11+ prevention programme which has a substantial injury-preventing effect by reducing football injuries by 39%, whereas a preventive effect of the FIFA 11 prevention programme could not be documented. PROSPERO CRD42015024120.