This paper presents a new active in-flight rotorblade tracking control system for helicopters equipped with trailing-edge flap actuators on the rotor blades. The objective of the in-flight rotorblade tracking controller is to minimize vibrations in the helicopter cabin and vibratory loads at the rotor hub induced by static blade dissimilarities. The control design is based on a steady-state transfer matrix from flap inputs to vibration outputs, which is first identified experimentally and then symmetrized. For this design model, an analytically derived Moore–Penrose pseudoinverse, which plays a key role in overcoming restrictions of existing approaches, such as the dependency on full-rank transfer matrices, is used. The system is verified through flight tests carried out with a full-scale experimental helicopter. The results demonstrate that the presented in-flight tracking system effectively minimizes the tracking error induced vibrations.