Background: To evaluate the efficacy and safety of outpatient exercise training in clinically stabilized patients with chronic thromboembolic pulmonary hypertension (CTEPH) after balloon pulmonary angioplasty (BPA). Methods: Twenty-four patients with CTEPH after BPA were enrolled in this prospective single-center study. Patients were assigned to the exercise and control groups. The exercise group comprised 12 patients who received 15 weeks of exercise training, with usual care. The control group received only the usual care, without exercise training. The exercise program included aerobic exercise thrice weekly and resistance exercise once or twice weekly. The assessments employed included a 6-min walk test, cardiopulmonary exercise testing, and an emPHasis-10 questionnaire. Results: In the exercise group, the 6-min walk distance was significantly longer (510.0 [467.5, 595.0] m vs. 425.0 [395.0, 465.0] m, p = 0.020), the time taken to walk 10 m was shorter (6.4 [5.9, 7.5] s vs. 8.9 [8.1, 9.1] s, p = 0.020), and the walking speed was faster (1.6 [1.3, 1.7] m/s vs. 1.1 [1.1, 1.2] m/s, p = 0.020) at 15 weeks compared with the results for the control group. The quality of life tended to improve at 15 weeks compared with that before the exercise training. However, hemodynamics did not change significantly before and after the exercise training, and no fatal arrhythmias or syncope were observed. Conclusions: Exercise training improved gait performance, without any adverse events, in patients with CTEPH after BPA. Therefore, exercise training as an adjunct to medical therapy may be a safe potential therapy for patients with CTEPH after BPA.