Patients with chronic kidney disease reportedly have decreased muscle oxygen utilization, which most substantially decreases exercise capacity, followed by cardiac reserve. However, determinants of longitudinal changes in exercise capacity in patients on hemodialysis and the effects of long-term exercise interventions are unknown. This study was conducted to clarify these concerns. This was a prospective cohort study. Patients on hemodialysis that were not hospitalized were followed from baseline up to 2years, and cardiopulmonary exercise testing results, including peak oxygen uptake, peak work rate, heart rate reserve, and ventilatory equivalent for carbon dioxide slope, as well as implementation of exercise interventions were assessed. Based on the 2-year change in peak oxygen uptake, they were divided into improvement or declined groups. Forty-five patients who were not hospitalized completed the follow-up were analyzed. In the improvement group, the variation was determined by an increase in peak work rate, which is a peripheral factor (partial regression coefficient 0.08 [95% CI = 0.01 to 0.16]), while in the decline group, the variation was determined by a decrease in the ventilatory equivalent for carbon dioxide slope, which is a cardiac factor (partial regression coefficient = -0.12; 95% CI = -0.21 to -0.03). Moreover, exercise intervention was associated with the change in peak oxygen uptake (partial regression coefficient = 3.09; 95% CI = 1.45 to 4.72). Exercise intolerance even in patients on hemodialysis that were not hospitalized and stable progressed over time with deterioration of cardiac reserve, whereas exercise interventions were associated with improved exercise capacity through enhanced peripheral function. The results support the early measurement of cardiopulmonary or skeletal muscle reserve through cardiopulmonary exercise testing and the implementation of long-term exercise interventions based on the measurement results to address the potential deterioration in exercise capacity associated with reduced cardiac reserve, even in patients on hemodialysis that are asymptomatic and stable.