The objectives of this network meta-analysis were: (a) to estimate and compare the pooled effects of some injury prevention programs (IPPs) whose exercise-based components were categorized using a movement pattern-specific taxonomy on reducing overall and some specific body regions (lower extremity, thigh, knee, and ankle) injury incidences in youth team sport athletes and (b) to explore the individual effects of these components on the injury incidence rates (IIRs) previously mentioned. Searches were performed in PubMed, Web of Science, SPORTDiscus, and Cochrane Library. Eligible criteria were: exercise-based interventions comprised of exercises involving athletic motor skill competencies and evaluated against a control group, overall IIRs were reported, and youth (≤19 years old) team sport players. For the current analysis, a taxonomy based on movement patterns was employed for exercise component identification (upper body pushing and pulling; lower body concentric and eccentric; core; mechanics; acceleration; and lower body stability). Pooled effects were calculated by frequentist random effects pairwise and network meta-analyses. Nineteen studies were included. Most of the IPPs exhibit risk reduction when compared to their control groups on overall, lower extremity, and ankle injuries. Interventions comprised of lower body concentric and eccentric, core, mechanics, and lower body stability exercises were the most effective measures for reducing these injuries. None of the IPPs demonstrated to be effective for reducing thigh injuries, and contradictory results were found for knee injuries. Individual analysis at component level revealed that the lower body (bilateral and unilateral, concentric, and eccentric) component was the only one associated with a significant reduction on overall injuries. Indirect evidence suggests that interventions incorporating lower body concentric and eccentric, core, mechanics, and lower body stability exercises might be the most effective for reducing overall, lower extremity, and ankle injuries in youth team sports.