An active trailing-edge flap system for helicopter rotor blades using pneumatic artificial muscles was investigated, with the goal of generating flap deflections suitable for both vibration mitigation and primary flight control. Prior work with these actuators showed that large deflections were possible under full-scale conditions. This study developed and demonstrated an inner loop feedback controller that enables the flap to track the complex waveforms required to achieve its goal. Control algorithm development began with proportional feedback, but required the addition of a dead time compensator to reduce tracking error and increase bandwidth. The dead time compensator initially had a fixed value, though this transitioned to a variable to cope with potential changes in the dead time due to changing operating conditions. In this case, the system can continuously adjust the dead time estimate from the position error and predict future tracking error using that estimate, and adjust the control action accordingly. This approach requires no system model and no a priori information about the desired command signal. As such, it is well suited to the active rotor problem. Testing of this controller on single sine waves and complex waveforms composed of a sum of the first four odd harmonics of the rotor frequency showed good tracking for all conditions.