This paper proposes a fusion controller combing an anti-windup PID controller and BELBIC (Brain Emotional Learning Based Intelligent Controller) for controlling the position and vibration of a robot system having a single flexible manipulator. A finite element model of the flexible manipulator is developed. The reliability of it is verified by comparing the natural frequencies computed using the finite-element method with the experimentally measured ones. An MSC.ADAMS computational model of the robot system is interfaced with the proposed controller in MATLAB/Simulink, for carrying out a simulation. The simulation is performed with various references inputs and endpoint masses. The effectiveness and robustness of the proposed controller for control of the position and vibration of the flexible manipulator is shown through the simulation.