Chronic obstructive pulmonary disease (COPD) has significant systemic effects, such as weight loss, which affects exercise capacity, health-related quality of life (HRQOL) and survival. The traditional herbal medicine, Hochuekkito (TJ-41), improves the nutritional status and decreases systemic inflammation in patients with COPD. However, to date, the additive effect of TJ-41 on pulmonary rehabilitation (PR) in patients with COPD has not been researched comprehensively. The purpose of the present study was to investigate the efficacy and safety of adding TJ-41 to PR for patients with COPD. Thirty-three malnourished patients with COPD were randomly assigned to receive low-intensity exercise with (TJ-41 group) or without (control group) TJ-41 treatment for 12 weeks. The primary outcome was the change in the 6-min walk distance (6MWD). Secondary outcomes included changes in the body composition, peripheral muscle strength, modified Medical Research Council dyspnea score, visual analog scale (VAS) score for dyspnea, VAS score for fatigue and COPD assessment test (CAT) score. After the 12-week treatment, body weight and percent ideal body weight were significantly increased in the TJ-41 group (P<0.05), but not in the control group. After the 12-week treatment, the modified Medical Research Council dyspnea score, VAS score for dyspnea, VAS score for fatigue and total CAT score decreased significantly in the TJ-41 group (all P<0.05), but not in the control group. There were no significant differences in the 6MWD and peripheral muscle strength between baseline and after 12 weeks of treatment in either group. No adverse effects were noted with the use of TJ-41. It was concluded that the addition of TJ-41 to PR may benefit malnourished patients with COPD with respect to dyspnea and HRQOL.