Background: Exercise training has positive effects on physical functions and could reduce a sedentary lifestyle for hemodialysis (HD) patients. Given that low-level physical activity increases morbidity and mortality, here, we aimed to determine the effects of an intradialytic exercise program delivered at different frequencies on HD patients in Taiwan. Methods: This study is a prospective, randomized control trial. An intradialytic exercise program will be arranged for patients after receiving their informed consent. Patients will be segregated at random into three groups as follows: (a) three times/week of intradialytic exercise training plus standard care maintenance of HD, (b) two times/week of intradialytic exercise training plus standard care maintenance of HD, or (c) standard care maintenance of HD. Subjects will be followed for 24 weeks. At three time points, 0, 12, and 24 weeks, the primary outcome, the Short-Form 36 score, will be measured. Additional secondary outcomes to be measured are the Beck depression inventory, 6 min walking test, sit-to-stand test, and anthropometric measures such as the body mass index, thigh circumference, and the proportion of fat in the body composition. Conclusions: There is emerging evidence in support of intradialytic exercise improving health-related quality of life for patients on HD. However, the difference in the therapeutic effects between three times per week and twice per week has never been determined. With this study, we anticipate to fill the knowledge gap in the exercise prescription among HD patients.