Flexible joint robot (FJR) manipulators can offer many attractive features over rigid manipulators, including light weight, safe operation, and high power efficiency. However, the tracking control of the FJR is challenging due to its inherent problems, such as underactuation, coupling, nonlinearities, uncertainties, and unknown external disturbances. In this article, a terminal sliding mode control (TSMC) is proposed for the FJR system to guarantee the finite-time convergence of the systems output, and to achieve the total robustness against the lumped disturbance and estimation error. By using two coordinate transformations, the FJR dynamics is turned into a canonical form. A cascaded finite-time sliding mode observer (CFTSMO) is constructed to estimate states and lumped disturbance in a finite time based on two measurable states, which not only attenuates the measurement noise but also reduces the peaking phenomenon. The closed-loop stability and the finite-time convergence are rigorously proved by using Lyapunov theorem. The upper bound of the finite convergence time is derived for the reaching and sliding phase. Comparative study is conducted experimentally in real time on the FJR manipulator to verify the effectiveness of the proposed control method.