Due to their good performance reported in the field, there has been increased popularity in polymer modified binder mixtures. In the new Mechanistic-Empirical Pavement Design Guide (MEPDG), however, design procedures appear to attribute only moderate performance improvements to them, particularly for permanent deformation. A relationship is utilized in the MEPDG for permanent deformation in layers of hot mix asphalt (HMA) that include mix characteristics effects only through asphalt concrete mix dynamic modulus. It is suggested, however, through evidence in the literature that dynamic modulus use alone may be insufficient for complete HMA permanent deformation behavior characterization. The authors present permanent deformation analysis of mixes prepared under different conditions with modified and virgin binders using confined axial permanent and dynamic modulus deformation tests. Test results are used for modified binder and other mix characteristic effect evaluation in regard to permanent deformation model parameters. For potential improvement evaluation in performances of modified binder mixes over those with unmodified binders, the MEPDG is then run with field condition-adjusted modified parameters. That laboratory test-based permanent deformation model parameters adjustment provides prediction of modified mix performance improvements over unmodified mixes more in line with literature-reported improvements is shown in this work. How other mix characteristic may offset or complement modified binder improvement is also explored. It is suggested by the study that for proper HMA permanent deformation behavior modeling, modeling needs to be complemented by either permanent deformation model parameters or permanent deformation tests that are a function of binder types and other mix characteristics.