This paper presents the results of attitude control of flexible spacecraft using Pulse Width Pulse Frequency (PWPF) modulated thruster. The control object in this paper is the U.S. Naval Postgraduate School's Flexible Spacecraft Simulator (FSS), which is comprised of a rigid central body and a flexible appendage. Simulations show that the use of pulse-width pulse-frequency modulated thrusters provides several important advantages over conventional bang-bang thruster control, including less thruster activity, smoother control action, and closer-to-linear actuation. The control loop design in the presence of structural flexibility and possible interaction with the PWPF modulator nonlinearity are addressed. Using a describing function model of the modulator, the stability margin with respect to the structure mode limit cycle is predicted in the control design. Simulations show that the predicted stability margin is conservative but acceptable.