During the chemical ordering of the high anisotropy FePt L10 phase a fcc-→fct structural distortion in the unit cell occurs. Monitoring the stress relaxation time dependencies during isothermal annealing cycles may lead to a better understanding of the L10 ordering kinetics thickness dependencies in thin FePt films. During the isothermal portion of the anneal cycle all films showed an exponentially decaying stress relaxation with time to lower compressive stress states for all temperatures and thickness. The stress relaxation rate increased significantly with an increase in Fe51Pt49 film thickness and annealing temperature. Stress relaxation activation energies of 2.21 eV, 2.40 eV, and 2.96 eV for the 50nm, 25nm, and 10nm Fe51Pt49 films, respectively, were extracted. This correlated well with the observed trends in the post annealed film coercivity, increase of the (001) superlattice L10 peak, and the shifting of the (111) peak position, all indicators of L10 chemical ordering transformation.