The aim of this study was to examine the effects of a 12-week home-based exercise program on physical function, psychological dimensions, and health-related quality of life for patients with chronic kidney disease. Ninety eligible patients were enrolled and randomly separated into the exercise group and the control group from November 2015 to May 2016. The exercise group received an individualized exercise program while the control group received only usual care and continued primary lifestyle. Physical function was measured using 6-minute walk test and 10 repetitions of the sit-to-stand test while psychological dimensions were assessed by the Hospital Anxiety and Depression scale and the Self-Efficacy for Exercise scale. Quality of life was evaluated by a disease-specific instrument, the Kidney Disease Quality of Life scale. The differences between the exercise group and the control group were statistically significant for 6-minute walk distance, the time to complete 10 repetitions of the sit-to-stand test, self-efficacy for exercise, anxiety and depression, and all domains of health-related quality of life after a 12-week exercise. This study suggests that home-based individualized exercise program is an effective and feasible way of improving physical function, psychological stress, and health-related quality of life for early stage of chronic kidney disease patients.