Pitch loop control is the fundamental tuning step for vertical takeoff and landing (VTOL) unmanned aerial vehicles (UAVs), and has significant impact on the flight. In this paper, a fractional order strategy is designed to control the pitch loop of a VTOL UAV. First, an auto-regressive with exogenous input (ARX) model is acquired and converted to a first-order plus time delay (FOPTD) model. Next, based on the FOPTD model, a fractional order [proportional integral] (FO[PI]) controller is designed. Then, an integer order PI controller based on the modified Ziegler-Nichols (MZNs) tuning rule and a general integer order proportional integral derivative (PID) controller are also designed for comparison following three design specifications. Simulation results have shown that the proposed fractional order controller outperforms both the MZNs PI controller and the integer order PID controller in terms of robustness and disturbance rejection. At last, ARX model based system identification of AggieAir VTOL platform is achieved with experimental flight data.