An adaptive active disturbance rejection control is proposed for flexible manipulators with uncertain payload. The two-time scale model of the multiple-flexible-link manipulator is derived via singular perturbation technique. For the fast subsystem, a linear quadratic regulator controller is designed. It depresses the oscillation of flexible links and drives the states to the slow manifold quickly. For the slow subsystem, an adaptive active disturbance rejection controller is proposed to track the desired angular position. A recursive least-squares algorithm is utilized to estimate the payload mass and compensate for the uncertainty. Simulation results show that the mean squire error is less than 0.08 rad even when the payload uncertainty up to 200% of the pre-estimation of the payload mass, which is superior to the case without compensation for the payload uncertain. Thus, the proposed control scheme guarantees a robust performance in presence of uncertain payload and under different maneuver speeds.