In this paper, vibration suppression of a flexible beam on a moving cart is investigated based on fractional order disturbance observers (FODOB). Linear models to describe the position of the beam-cart system and the single-mode vibration of the beam are firstly derived. Likewise, a fractional order model is also identified for such a vibration, which is considered as a disturbance of the cart. The proposed control strategy consists of a proportional-derivative (PD) controller with noise filter to control the position of the cart, and a FDOB to compensate the coupling torque between the flexible beam and the cart. Simulation results are given to show the effectiveness of the proposed strategy to attenuate the vibration of the beam.