This research effort develops a guidance and control system for a small airship to fly through assigned waypoints in three dimensional space with a desired speed in the presence of wind and wind gust. In the control system development and validation, a simulation environment based on the nonlinear 6-DOF model of an airship, including the effect of the wind, is used. The controller design is based on MIMO (Multi-Input Multi-Output) LQR (Linear Quadratic Regulator) method. A gain scheduling scheme is used to cover multiple operating conditions based on the forward speed. Nonlinear simulations for different scenarios are performed and results are discussed. The simulation experiments show that the airship can fly through the assigned waypoints, even when the way points are at different altitudes,