The purpose of this study was to investigate the immediate effects of traditional Thai massage (TTM) on stress-related parameters including heart rate variability (HRV), anxiety, muscle tension, pain intensity, pressure pain threshold, and body flexibility in patients with back pain associated with myofascial trigger points. Thirty-six patients were randomly allocated to receive a 30-min session of either TTM or control (rest on bed) for one session. Results indicated that TTM was associated with significant increases in HRV (increased total power frequency (TPF) and high frequency (HF)), pressure pain threshold (PPT) and body flexibility (p < 0.05) and significant decreases in self-reported pain intensity, anxiety and muscle tension (p < 0.001). For all outcomes, similar changes were not observed in the control group. The adjusted post-test mean values for TPF, HF, PPT and body flexibility were significantly higher in the TTM group when compared with the control group (p < 0.01) and the values for pain intensity, anxiety and muscle tension were significantly lower. We conclude that TTM can increase HRV and improve stress-related parameters in this patient population.