In this paper, the effects of velocity estimation on the tracking performance of a harmonic drive system are investigated. Harmonic drive gearing is an important element to precision motion systems that are needed to have lightweight. However, the harmonic drive gearing introduces compliance to the motion systems, and velocity feedback is required to increase system damping. In this paper, several nonmodel-based approaches to velocity estimation are revisited and practically applied to the tracking control of a harmonic drive system. Based on experimental results, their performance comparisons are done in terms of tracking precision and smoothness of estimation results.