A pulse detonation engine simulator operating at 5 and 20 Hz was used to study unsteady thrust characteristics. The natural vibration frequencies, the effective mass of the simulator and the steady thrust were first determined. The system dynamics of the simulator, deconvolved in the frequency domain, was studied. The impulse transfer function was used to reconstruct the thrust response and acceleration compensation was applied to get the thrust solely due to the pulsating jet. The thrust response of the system due to exit of the pulsed jet could be reconstructed well. The acceleration compensation technique enabled the actual thrust to be recovered from reconstructed signal. Pulse-to-pulse interference was not observed for the frequencies tested. The generated thrust along the axial direction was measured using a force sensor. A multi-axial compression type accelerometer was used to measure the acceleration of the entire simulator. And force plate was used as thrust stand.