This work proposed a motion estimation method for a flexible robotic manipulator with a vision-based end-effector. The effectiveness of the proposed estimation method was evaluated by utilizing a non-linear dynamic model of a flexible manipulator using the co-rotational finite element method. This modeling utilized multiple co-ordinate (co-rotational) systems which rotated and translated with each element, allowing the investigation of flexible manipulator dynamics with the large rotational and translational motion. Smart piezoelectric sensors, embedded to the flexible manipulator, were used for vibration sensing purposes. Simulation results on a flexible manipulator demonstrated the feasibility of the proposed estimation method in predicting the movement of end-effector with a satisfactory accuracy. Experimental results confirmed the effectiveness of the estimation method. Results from the vision analysis, based on experimental results, demonstrated the feasibility of the estimation method for a further flexible manipulator application with the eye-in-hand system.