Aim: To examine the effects of parent-delivered traditional Thai massage (TTM) intervention on heart rate variability (HRV) and gait in children with autism. Methods: This was a two-armed, randomized controlled trial conducted at the Haikou Special Education School in Haikou Province, China, between October 2021 and March 2022. A total of 48 children with autism, aged between 7 and 12 years, were selected from the school and randomly divided into either the parent-delivered TTM group or the control group (no intervention) in a 1:1 ratio. In addition to their regular daily school routines, the TTM group received 16 TTM interventions (twice a week), with each session lasting approximately 50 min. HRV and gait parameters were measured at baseline, completion of the 8-week intervention, and 2 months follow-up. Results: The results of this study showed that the TTM intervention had a notable positive effect on HRV, with a significant reduction in low-frequency value (p = 0.001), and increased high-frequency value (p = 0.001), compared with the controls, and the advantages persisted during the follow-up period. However, only the stride length in the TTM group was significantly longer than that in the control group at the post-test (p = 0.039) and follow-up test (p = 0.043), while none of the other parameters of gait comparison showed statistical significance. Conclusions: Parent-delivered Thai massage increased HRV levels and stride length in comparison to the control group, and some effects of the intervention were maintained over the follow-up period. Clinical Trials Registry Identifier ChiCTR2100051355; September 21, 2021.