Cardiac rehabilitation (CR) can reduce cardiovascular mortality and morbidity in coronary artery disease. Long coronary artery lesions may be associated with adverse outcomes after drug-eluting stent (DES) implantation. The purpose of this study was to evaluate angiographic outcomes after a comprehensive CR program in patients with DESs for long coronary artery lesions. A total of 576 patients treated with DESs for long (≥25 mm) coronary lesions were enrolled in this prospective CR registry. Comprehensive CR programs were successfully performed in 288 patients (50%). The primary end point was in-stent late luminal loss at the 9-month angiographic follow-up. There were few significant differences between the CR and non-CR groups in terms of baseline characteristics, including clinical, angiographic, and procedural variables. The rate of in-stent late luminal loss in the CR group was 35% less than in the usual care group (0.19 ± 0.33 mm in CR vs 0.29 ± 0.45 mm in non-CR, difference 0.08 mm, 95% confidence interval 0.01 to 0.16, p = 0.02) at the 9-month follow-up. After propensity-matched analysis (224 pairs), the results were consistent (0.18 ± 0.31 mm in CR vs 0.28 ± 0.41 mm in non-CR, difference 0.10 mm, 95% confidence interval 0.02 to 0.18, p = 0.02). The CR group showed a significant improvement in the overall risk profile compared with the non-CR group, including current smoking, biochemical profiles, depression, obesity, and exercise capacity. In conclusion, the comprehensive CR program significantly reduced late luminal loss after DES implantation for long coronary lesions. This may be associated with significant improvements in exercise capacity and overall risk profile.