Objective: Children with cerebral palsy (CP) have an impaired cardiac autonomic function. Attenuated heart rate recovery (HRR), which is a valuable prognostic parameter for autonomic nervous system, is known to be associated with an increased risk of cardiovascular events and all-cause mortality. However, only few studies have observed the effects of exercise on the cardiac autonomic function in children with CP. The purpose of this pilot study was to examine the effects of equine-assisted activity (EAA) program on cardiac autonomic function in children with CP. Design: A single-blinded, parallel, two-arm pilot trial with 1:1 randomization to the EAA or control group. Setting: A tertiary university hospital and a local arena. Subjects: Twenty-six children with CP (Gross Motor Function Classification System Levels I-II). Intervention: Each lesson of the EAA program for the EAA group was conducted for 40 min twice a week, and the whole program duration was 16 weeks (a total of 32 sessions). Outcome measures: A graded exercise test was performed to measure the resting heart rate (RHR), HRR, and peak oxygen uptake (VO2peak) on both groups before and after the 16-week period. Results: The autonomic nervous function measured by the response of HRR improved at 1 min (p < 0.009), 3 min (p < 0.001), and 5 min (p < 0.004) only in the EAA group. RHR significantly improved in the EAA group (p < 0.013), whereas the VO2peak did not significantly differ between the two groups. Conclusion: The HRR and RHR of the children with CP improved after completing the 16-week EAA program. The results demonstrated that the program had a positive effect on the improvement of cardiac autonomic function in these patients. Clinical Trial Registration Number: NCT03870893.