Exercise intolerance and undue fatigue are common complaints in patients with Charcot-Marie-Tooth (CMT) disease. Reduced physical ability is due directly to the disease, but it is also due to physical deconditioning. The aim of this study was to test whether 24 weeks of interval-training exercise (ITE) cycling can significantly improve physiological, neuromuscular, and functional capacities and alleviate fatigue in CMT patients. Eight CMT patients (4 CMT1A and 4 CMT2) participated in ITE for 3 nonconsecutive days per week. Cardiovascular fitness, muscle strength, fatigue resistance, and functional capacities were measured before and after 12 weeks of supervised hospital training and again after another 12 weeks of unsupervised home training. Training was well tolerated. There were significant improvements in cardiorespiratory capacities, isokinetic concentric strength, and functional ability measurements. All patients experienced an improvement in their self-reported visual analogic scale for fatigue and pain during training. However, there was no significant change in their isometric force production and indices of fatigue resistance after training. Although the improvement in exercise tolerance may be due in part to reversal of the deconditioning effect of their related sedentary lifestyle, this clinical trial suggests that ITE can benefit CMT patients especially in their functional performance and subjective perception of pain and fatigue. Moreover, the improvement observed at the end of the first supervised period ITE was maintained after the second unsupervised home period, although there was no further improvement in performance and tolerance.