Aims The efficacy and safety of cardiac rehabilitation for patients with persistent atrial fibrillation who restored sinus rhythm after catheter ablation remains unclear. The aim of the present study was to evaluate the effects of cardiac rehabilitation on exercise capacity, inflammatory status, cardiac function, and safety in patients with persistent atrial fibrillation who had catheter ablation. Methods In this randomized controlled study, 61 patients treated with catheter ablation for persistent atrial fibrillation (male, 80%; mean age, 66 ± 9 years) were analyzed. Thirty patients underwent cardiac rehabilitation (rehabilitation group), whereas the remaining 31 patients received usual care (usual care group). The rehabilitation group underwent endurance and resistance training with moderate intensity, at least three times per week for six months. Six-minute walk distance, muscle strength, serum high-sensitivity C-reactive protein, plasma pentraxin 3, left ventricular ejection fraction and atrial fibrillation recurrence were assessed at baseline and at six-month follow-up. Results In the rehabilitation group, significant increases in the six-minute walk distance, handgrip strength, leg strength and left ventricular ejection fraction and significant decreases in high-sensitivity C-reactive protein and plasma pentraxin 3 concentrations were observed at six-month follow-up compared with baseline (all p < 0.05). No significant changes were observed in the usual care group. During the six-month follow-up period, the number of patients with atrial fibrillation recurrence was six (21.4%) in the rehabilitation group and eight (25.8%) in the usual care group (risk ratio, 0.83; 95% confidence interval, 0.33 to 2.10). Conclusions Cardiac rehabilitation improved exercise capacity without increasing the risk for atrial fibrillation recurrence. It may also be effective in managing systemic inflammatory status and systolic left ventricular function in patients with persistent atrial fibrillation treated with catheter ablation.