The use of robots in rehabilitation has become an issue of increasing importance because of the requirement of functional recovery therapy for limbs. A novel pneumatic artificial muscle (PAM) actuator - which has achieved increased popularity for providing safety and mobility assistance to humans performing tasks, as well as providing another advantages such as high strength and power/weight ratio, low cost, compactness, ease of maintenance, cleanliness, readily available, cheap power source, and so on - has been considered during the recent decades for use in a therapy robot, which in particular requires a high level of safety. However, some limitations still exist, such as air compressibility and the lack of damping ability of the actuator to bring the dynamic delay of the pressure response and cause the oscillatory motion. In addition, to aid rehabilitation more efficiently, the robot should adjust its impedance parameters according to the physical condition of the patient. For this purpose, the manipulator join is equipped with a Magneto-Rheological Brake (MRB). A new phase plane switching control method using MRB is proposed for tracking sinusoidal waveforms. The effectiveness of the proposed algorithm is demonstrated through an experiment using a fabricated two-axis PAM manipulator. The experiment proves that the stability of the manipulator could be greatly improved using a high gain control without regard to the change of the frequencies of the reference input and the external load condition, and without decreasing the response speed or lowering the stiffness of PAM manipulator.