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Important nonlinear transmission attributes exhibiting coupled dynamics and deteriorating performance of harmonic drive systems include hysteresis and kinematic error. This work presents control algorithms developed to compensate for hysteresis in the presence of kinematic error (KE) for precision position tracking applications with known smooth load on the output side. A model of hysteresis with a linear flexibility part and nonlinear dissipative part represented by a differential equation is used. The model is integrated with kinematic error model to obtain a set of equations governing system dynamics. First, a singularly perturbed model of the drive is derived from this set of equations. The proposed algorithm is then developed using integral manifold control approach involving slow and fast control terms. A recent result by authors on compensation of kinematic error alone is employed for the same. Simulation results with the proposed algorithms establish its effectiveness.