A new cycle ergometer using a Magneto-Rheological (MR) rotary brake system has been developed for rehabilitation of hemiplegia patients to reduce uneven pedaling characteristics. For this purpose, a control method to adjust the resistance of the MR rotary brake in real time based on the magnitude of the muscular force exerted by the subject has been devised so that the mechanical resistance to the pedaling can be minimized when the affected leg was engaged for pedaling. A series of experiments were carried out with and without the engagement of this real-time control mode of MR rotary brake at different pedaling rate to find out the effect of the real-time control mode. The characteristics of the pedaling for these specific conditions were analyzed based on the variations in angular velocities of the pedal unit. The results showed that the variations in the angular velocities were decreased by 42.9% with the control mode. The asymmetry of pedaling between dominant and non-dominant leg was 19.63% in non-control mode and 1.97% in the control mode. The characteristics of electromyography(EMG) in the lower limbs were also measured. The observation showed that Integrated EMG(IEMG) reduced with the control mode. Therefore, the new bicycle system using MR brake with the real time control of mechanical resistance was found to be effective in recovering the normal pedaling pattern by reducing unbalanced pedaling characteristics caused by disparity of muscular strength between affected and unaffected leg.