In this paper, we prpose a method for tracking optimally a spatial trajectory of the end-effector of flexible robot arms with multiple joints. The proposed method finds joint trajectories and joint torques necessary to produce the desired end-effector motion of flexible manipulator. In inverse kinematics, optimized joint trajectories are computed from elastic equations. In inverse dynamics, joint torques are obtained from the joint euqations by using the optimized joint trajectories. The equations of motion using finite element method and virtual work principle are employed. Optimal control is applied to optimize joint trajectories which are computed in inverse kinematics. The simulation result of a flexible planar manipulator is presented.