A general, dynamical approach developed a high-fidelity, finite element model of a pulse detonation engine (PDE). The approach deconvolved the structural response due to cyclic acceleration that would be measured by a load cell, thereby obtaining the actual thrust that is produced. The model was excited with pressure pulses that simulated actual detonation pressure characteristics at different frequencies. A two-step process was developed. In the first step, the system dynamics was established and validated by deconvolving from a known input in the form of pressure pulses from which the reconstructed thrust output was obtained. The second step required that the deconvolved thrust be compensated for system acceleration. This step required the effective mass and induced acceleration to be determined which then yielded an inertial load that has to be removed from the reconstructed thrust to obtain the actual thrust. The compensated thrust values were expressed in the form of specific impulse for the PDE which compared well with a priori pulsed thrust loading.