Purpose To investigate the effect of an early postoperative outpatient cardiac rehabilitation program to health-related quality of life among heart transplantation recipients (HTR) and patients with coronary artery bypass graft (CABG) surgery. Methods The study included 45 clinically stable HTR (age: 47 ± 14 years; 36 men, 9 women) and 34 patients with CABG (age: 57.2 ± 12.5 years; 27 men, 7 women). HTR started rehabilitation 70 ± 33 days after transplantation; patients with CABG started training 36 ± 18 days after surgery. Patients participated in a 12-week supervised exercise training program three times per week. Each training session comprised 10 minutes of warm-up, 25 to 30 minutes of cycling or treadmill walking, and 10 minutes of cooldown. The exercise intensity was set at 50% to 80% of peak oxygen uptake (V̇O 2peak) according to the patient's condition. The health-related quality of life of subjects was evaluated by the Medical Outcomes Trust 36-item health survey (SF-36) at baseline and upon the completion of rehabilitation. Results At baseline, the HTR group showed lower V̇O 2peak than the CABG group, but the health-related quality of life was similar between the two groups. After training, both groups exhibited an increase of 3.6 mL · kg −1 · min −1 in V̇O 2peak and improvement of physical component in health-related quality of life. The HTR group showed a significant increase of SF-36 scores in physical functioning (59.7 ± 18.9 to 77.0 ± 14.0), physical role (21.1 ± 34.1 to 38.3 ± 37.9), bodily pain (57.4 ± 24.3 to 73.6 ± 21.5), social functioning (63.6 ± 23.4 to 72.8 ± 22.1), emotional role (59.2 ± 43.7 to 76.3 ± 37.4), and mental health (67.1 ± 17.9 to 73.4 ± 14.6). The CABG group only exhibited increased scores in physical functioning (60.0 ± 22.9 to 73.4 ± 18.0), physical role (19.1 ± 24.9 to 27.9 ± 38.3), bodily pain (57.1 ± 20.0 to 70.3 ± 16.1), and social functioning (54.0 ± 21.3 to 69.9 ± 21.1). Conclusions Early postoperative cardiac rehabilitation significantly improved physical capacity and quality of life among heart transplant recipients and patients with CABG. Additionally, HTR showed greater improvement in health-related quality of life than patients with CABG regardless of lower physical capacity.