The work presented in this paper addresses trajectory tracking and position control of a six-degrees-of-freedom flapping wing micro aerial vehicle (FWMAV) in the presence of matched and mismatched disturbances. FWMAV is an unstable system which is affected by various disturbances. These disturbances can be classified into matched and mismatched disturbances according to their entrance via the same or different channels from control inputs. In order to handle these disturbances, an integral command-filtered block backstepping controller is applied to a nonlinear high-fidelity time-variant dynamic model. The stability of the proposed controller and the ultimate boundedness of the tracking error is derived based on Lyapunov stability arguments. Finally, the control law is validated by various simulation studies on the high-fidelity model. The proposed controller performance proves its ability to successfully track the arbitrary desired reference trajectories with feasible control effort in the presence of both constant and time-varying matched and mismatched disturbances.