A co-simulation using ADAMS and MATLAB/ Simulink is proposed for the dynamic simulation of high speed rotating flexible rotor supported by active magnetic bearings. The controller and actuator of AMBs are modeled in MATLAB/Simulink and the plant model of the rotor is implemented in ADAMS software. A decentralized proportional - integral - derivative (PID) control is used as main position regulator. The electromagnetic actuator is modeled as linearized spring with constant position stiffness and current stiffness. The current amplifier is modeled as proportional current controller which drives electromagnet coils with constant DC voltage. The rotor is modeled as flexible body in ANSYS software and the ADAMS gives motions and mechanical constraints to this body, finally completes rotating flexible rotor model supported AMBs. The ADAMS plant model is incorporated to MATLAB/ Simulink as a s-function, and MATLAB do the simulations. In the co-simulation results, run-out values of the constantly rotating flexible rotor is calculated numerically, which is not reported in rigid body rotor dynamics.