A new approach to thrust measurement for pulse detonation engines (PDEs) was developed to account for the effects of system dynamics. The approach was applied to a PDE operating at 10 and 20 Hz. Important system parameters such as steady-state response, effective mass of PDE and thrust measurement rig structure, and mass flow rates of fuel/oxidizer were first determined. The system dynamics of the PDE, deconvolved in the frequency domain, was studied. The system's transfer function between the thrust and a corresponding pressure obtained by a single propagating detonation pressure history during a typical PDE operation was established and used to reconstruct the thrust response for pulsed operation. A proper reconstruction of the deconvolved thrust values was accomplished through this technique. The acceleration experienced by the PDE thrust measurement rig during a typical operation was also measured. This measured acceleration when multiplied by the determined effective mass gave an estimate of the inertial force. The estimated inertial force when subtracted from the deconvolved force gave actual thrust. The measured and compensated thrust were expressed in the form of impulse.