Background: As sedentary life increases, people's thoracic vertebra joint movement decreases, and the resulting associated pain is complaining of a lot of discomfort. This is also affecting the autonomic nervous system. Objectives: The purpose of this study was therefore to find out the effect of thoracic vertebra joint mobilization on heart rate variability in upper back pain patients. Design: Randomized controlled trial. Method: Thirty subjects in this study were randomly assigned to two groups of 15 persons each using a randomization tool. Maitland's grade III joint mobilization, hot pack, and interferential current therapy (ICT) were applied to T1-L2 and hot pack and ICT were applied to the control group. The intervention was performed 3 times a week for 4 weeks. Results: There were statistically significant changes in Visual Analog Scale (VAS), Standard Deviation of all Normal R-R Intervals (SDNN), Low Frequency (LF), High Frequency (HF) and LF/HF ratio in the study group, and statistically significant changes in VAS, SDNN, and LF/HF ratio in the control group. In comparison of differences, there were statistically significant changes in VAS. Conclusion: Positive effects were found on SDNN and LF/HF ratio in both the joint mobilization group and the control group compared to before the study. In particular, even LF and HF were positive in the joint mobilization group showed influence.