In this paper, an adaptive controller with structurally dynamic wavelet network is developed for a harmonic drive subject to parameter varying friction. The control architecture integrates a proportional controller, a feedback adaptive component and sliding component to adaptively compensate for the friction to achieve accurate position tracking. Global asymptotic stability of the algorithm is proved by using Lyapunov function. In parallel to the adaptive controller, a fuzzy reconfiguration scheme is devised to change the structure of the network along with weights updating to improve the system tracking performance and robustness. Experimental tests on a harmonic drive manipulator verify the effectiveness of the proposed control method.