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This paper studies a new boundary control strategy for a flexible manipulator subject to unknown fast time-varying disturbances. The flexible manipulator essentially is an infinite dimensional continuum. Hence, a continuous function of space and time can be employed to describe the position of such a distributed parameter structure, the motion of which can be described by partial differential equations (PDEs). To cope with fast time-varying external disturbances, a high order disturbance observer is adopted. A control strategy based on such a disturbance observer is proposed for the rest-rest maneuvering of the flexible manipulator. Moreover, a smooth hyperbolic function is included in the controller to satisfy the requirement of input saturation. The stability of the boundary control is analyzed using LaSalle's invariance principle. Finally, the performance of the presented boundary controller is verified through comparison with that of employing a constant disturbance observer via numerical simulations.