<p>Exercise interventions targeting Fundamental Movement Skills (FMS) represent a critical approach for mitigating functional impairments in children with autism spectrum disorder (ASD). This study, for the first time, based on motor development theory, employed a Network Meta-analysis (NMA) to examine the effects of four types of exercise interventions—Isolation of Fundamental Movement Skills (FMS-I), Combination of Fundamental Movement Skills (FMS-C), Fine Motor Movement (FMM), and Specialized Movement Skills (SMS)—on the core symptoms of ASD in children aged 3–12, including social communication deficits and stereotyped and repetitive behaviors. Five electronic databases were systematically searched up to May 22, 2024. Included studies compared exercise interventions with control groups and assessed at least one core symptom of ASD. Study quality and evidence certainty were evaluated using the Risk of Bias tools (RoB 2.0, ROBINS-I) and the Confidence in Network Meta-Analysis (CINeMA) framework. Data analysis was performed via Stata 17.0 software. The systematic review included 26 studies encompassing 878 children, with 19 studies eligible for NMA. Ranking probabilities indicated that FMS-I emerged as the most promising intervention for addressing social communication deficits (SMD: -0.99, 95%CI: -1.46 to -0.52; SUCRA: 86.9%) and stereotyped and repetitive behaviors (SMD: -2.73, 95% CI: -3.76 to -1.70; SUCRA: 100%). The FMS-C showed potential for enhancing overall features (SMD: -0.90; 95%CI: -1.32 to -0.49; SUCRA: 74.7%). To conclude, exercise interventions should be grounded in FMS, transitioning from isolated movements to integrated actions, to enhance the overall behavior of children with ASD.</p>