Background: Poor health-related physical fitness (HRPF) and overweight and obesity are common health problems for children with intellectual disability. This study aimed to review existing lifestyle intervention studies, and identify effective strategies for this population. Methods: A systematic search was undertaken in three databases. The random-effects model was used to pool the weighted results by inverse variance methods, and the I2 statistic was applied to assess heterogeneity among the included studies. Results: Most of the identified interventions (27/29) adopted physical activity (PA). For obesity-related outcomes, the results showed no significant effect of PA studies on reducing obesity. For HRPF outcomes, significant effects were found on 6-min walk distance (51.86 m, 95% CI [16.49, 87.22], p < 0.05). Conclusions: PA is the predominant intervention component adopted and may contribute to improving cardiopulmonary fitness; but the lack of research limits our ability to draw any confirmed conclusion on obesity-related outcomes and other HRPF outcomes.