OBJECTIVE: Major depressive disorder is a common psychiatric condition characterized by persistent sadness and a lack of interest in life. It is often associated with alterations in autonomic nervous system functioning. This study examined the impact of a 10-week Baduanjin exercise program on heart rate variability and depression severity in individuals with major depressive disorder. METHODS: The present study was a two-arm, single-blind, pilot randomized controlled trial. Thirty-four participants were randomly assigned to either a Baduanjin group (n = 17) or a control group (standard care) (n = 17). The Baduanjin group participated in 60-minute sessions twice weekly while the control group were given the standard care appropriate for people with major depression disorder. Heart rate variability (HRV) and depression severity were assessed at baseline, Week 5, and Week 10. RESULTS: Results showed no significant interaction effect between group and time. However, there was a group effect for ratio of low-frequency-to-high-frequency (LF/HF ratio) HRV ( CONCLUSION: These findings suggested that Baduanjin exercise may positively influence aspects of autonomic function. Future research with larger sample sizes and longer follow-up periods is needed to investigate its long-term effects and potential benefits for depressive symptoms in individuals with major depressive disorder. This study was registered with the Chinese Clinical Trial Registry (ChiCTR1900027222).