The present article aimed to systematically summarize primary school-based intervention programs and their effects evaluated through randomized-controlled trial design. A systematic review of relevant articles was carried out using 4 electronic databases. From a total of 193 studies initially found, 30 were included in the qualitative synthesis. Main results: (1) Intensive interval training or jump/strength exercises may positively influence physical fitness, promoting challenging task, psychological needs, and guided styles to a greater extent; (2) Games that demand more cognitive function seem more beneficial than those based on repetitive aerobic exertion to improve fundamental motor skills; (3) The jumping/strength exercises may cause benefits in bone area and bone mineral density, while flexibility and balance may reduce the risk of muscle injury; and (4) Programming a greater dose of moderate-to-vigorous physical activity seems to be related to positive effects in core executive function and academic performance. Additionally, providing information and involving the social environment may enhance the positive effects.