The aim of this multicenter randomized controlled trial was to compare physiotherapist‐led exercise‐based cardiac rehabilitation (PT‐X) with physical activity on prescription (PAP) with regard to physical fitness, physical activity, health‐related quality of life (HR‐QoL), and metabolic risk markers in patients with permanent atrial fibrillation. Ninety six patients (28 women), age 74 (5) years, and ejection fraction ≥45% were randomized. An exercise tolerance test (primary outcome measure), muscle endurance tests, HR‐QoL, physical activity assessments (questionnaire and accelerometer), and blood sampling were performed. The PT‐X consisted of 60‐minute group sessions and home‐based exercise, both twice a week. The PAP consisted of 40 minutes of active walking, 4 times a week. Eighty seven patients completed the study. Exercise tolerance (maximum exercise capacity) improved significantly after PT‐X (n = 40) but not after PAP (n = 47) (16 vs −3 W; P < .0001). Muscle endurance also improved after PT‐X: shoulder flexion left arm (7 vs −1 repetition; P < .001), heel‐lift right leg (4 vs 1 repetition; P < .05), left leg (4 vs −1 repetition; P < .001), and shoulder abduction (17 vs −4 s; P < .010). PAP significantly increased energy expenditure. Health‐related quality of life and lab‐tests did not differ. PT‐X improved physical fitness in patients with permanent atrial fibrillation.