Objective: Determine if exercise interventions, beyond what is already provided to children and preschool children, improve bone health and reduce fracture incidence. Design: Systematic review and meta-analysis reported using the PRISMA guidelines. Certainty of evidence was assessed using GRADE recommendations. Data sources: Five electronic databases were searched for records: PUBMED; CINAHL; CENTRAL; SPORTDiscus; Web of Science. Eligibility criteria for selecting studies: Randomised, quasi-randomised and non-randomised controlled trials (including cluster-randomised) assessing the impact of additional exercise interventions (e.g., increased physical education classes or specific jumping programs) on bone health in children (6–12 years) and pre-school children (2–5 years) without dietary intervention. Results: Thirty-one records representing 16 distinct clinical trials were included. Dual-energy X-ray Absorptiometry (DXA) and/or peripheral Quantitative Computed Tomography (pQCT) were used to quantify bone health. Increased femoral neck bone mineral content in children with additional exercise interventions (n = 790, SMD = 0.55, 95% CI = 0.01 to 1.09) was reported, however this was not significant following sensitivity analysis. Other DXA and pQCT measures, as well as fracture incidence, did not appear to significantly differ over time between intervention and control groups. No studies reported adverse events. Studies failed to report all domains within the TIDieR checklist. All studies were at high risk of bias using the Cochrane RoB Tool 2.0. The certainty of the evidence was very low. Conclusions: The addition of exercise interventions, beyond what is provided to children, does not appear to improve DXA and pQCT measures of bone health. The effect of additional exercise interventions on bone health in pre-school children is largely unknown. Future trials should ensure adherence is clearly reported and controlled for within analysis as well as including reports of adverse events (e.g., apophysitis) that occur due to increased exercise interventions.