In this paper, a novel fault‐tolerant finite frequency H∞ controller (FFHC) is developed for uncertain mechanical system with input delay and constraint. First, the mathematical model of uncertain mechanical system is derived, where the uncertainties occur in mass, damping and stiffness matrices, respectively. Then, in view of the fact that the dominant resonance energies are caused by low‐order vibration modes of mechanical system, the finite frequency control algorithm is investigated to suppress these low‐order resonances peaks. By virtue of Lyapunov‐Krasovskii functional (LKF) and generalized Kalman‐Yakubovich‐Popov (GKYP) lemma, the desirable fault‐tolerant controller can be obtained by convex optimization. Numerical simulations verify the improvements and advantages of proposed cotroller in disturbance rejection when compared with the classic entire frequency H∞ controller (EFHC).