To explore the effect of exercise intervention on fundamental movement skills (FMS) of children with attention deficit hyperactivity disorder (ADHD) and/or autism spectrum disorder (ASD). Following the principle of PICOS, randomized controlled trials of the effect of exercise intervention on the FMS of ADHD/ASD children were searched. A total of 12 articles and 396 participants were included. Review Manager5.4 and Stata16.0 software were used to process and analyze the data. The results revealed that (1) exercise intervention can improve the gross motor skills of children with ADHD/ASD (p < 0.00001). Aquatic therapy (SMD = 56.54, 95% CI = 38.83–74.25) has a better effect on stability skills, and FMS intervention (SMD = 17.58, 95% CI = 1.78–33.38) has a better effect on locomotor skills and object control skills. (2) Exercise intervention can improve the fine motor skills of children with ADHD/ASD (p = 0.001). Table tennis exercise (SMD = 9.91, 95% CI = 0.23–19.59) and horse-riding program (SMD = 9.50, 95% CI = 5.20–13.80) have better effects on fine manual control and hand–eye coordination. (3) The closed-skill intervention for 60 min each time, twice a week, for at least 12 weeks had the best effect on the improvement in the FMS in children with ADHD/ASD (p < 0.00001). Exercise intervention may effectively improve FMS in children with ADHD/ASD. Intervention form, time, frequency, and duration are important moderator variables that positively impact the FMS of children with ADHD/ASD.