Right ventricular (RV) function is a prognostic factor in ischemic heart disease (IHD) patients, although its correlations with exercise capacity and cardiac rehabilitation (CR) efficacy are unknown. We aimed to clarify how RV function was associated with exercise tolerance and efficacy of phase II CR in IHD patients. We retrospectively analyzed 301 consecutive IHD patients who underwent phase II CR. We defined RV dysfunction using a combination of RV fractional area change < 35%, tricuspid annular plane systolic excursion < 1.6 cm, and systolic velocity < 10 cm/s. Exercise capacity was assessed using cardiopulmonary testing. The relation between RV function and exercise capacity was analyzed. The all-cause death and major adverse cardiac events (MACE) were evaluated by survival curve. The RV dysfunction group (n = 121) showed impaired left ventricular (LV) systolic and diastolic function before CR contrary to the normal RV function group (n = 180). The presence of RV dysfunction significantly reduced %AT by 4% and %Peak\(\dot{V}{\text{O}}_{ 2}\) by 9% before CR, but increases the degree of improvement in %Peak\(\dot{V}{\text{O}}_{ 2}\) with CR, independent of LV systolic and diastolic function. Univariate analysis demonstrated that previous coronary artery bypass grafting (CABG) was negatively associated with all-cause deaths and MACE. Adjusted for previous CABG, poor prognosis correlated with coexisting LV and RV dysfunction (hazard ratio [HR] 3.91, 95% confidence interval [CI] 1.13–13.53, P = 0.03) and RV dysfunction alone (HR 3.08, 95% CI 1.01–9.37, P = 0.05). In IHD patients, RV dysfunction is associated with exercise intolerance before CR and increased MACE risk, independent of LV function. The CR was effective in patients with RV dysfunction.