Abstract In this study, the passivity‐based robust control and tracking for Hamiltonian systems with unknown perturbations by using the operator‐based robust right coprime factorisation method is concerned. For the system with unknown perturbations, a design scheme is proposed to guarantee the uncertain non‐linear systems to be robustly stable while the equivalent non‐linear systems is passive, meanwhile the asymptotic tracking property of the plant output is discussed. Moreover, the design scheme can be also used into the general Hamiltonian systems while the simulation is used to further demonstrate the effectiveness of the proposed method.