Over the past few decades, the enhancement of polymer thermal conductivity has attracted considerable attention in the scientific community due to its potential for the development of new thermal interface materials (TIM) for both electronic and electrical devices. The mechanical elongation of polymers may be considered as an appropriate tool for the improvement of heat transport through polymers without the necessary addition of nanofillers. Polyimides (PIs) in particular have some of the best thermal, dielectric, and mechanical properties, as well as radiation and chemical resistance. They can therefore be used as polymer binders in TIM without compromising their dielectric properties. In the present study, the effects of uniaxial deformation on the thermal conductivity of thermoplastic PIs were examined for the first time using atomistic computer simulations. We believe that this approach will be important for the development of thermal interface materials based on thermoplastic PIs with improved thermal conductivity properties. Current research has focused on the analysis of three thermoplastic PIs: two semicrystalline, namely BPDA-P3 and R-BAPB; and one amorphous, ULTEM. To evaluate the impact of uniaxial deformation on the thermal conductivity, samples of these PIs were deformed up to 200% at a temperature of 600 K, slightly above the melting temperatures of BPDA-P3 and R-BAPB. The thermal conductivity coefficients of these PIs increased in the glassy state and above the glass transition point. Notably, some improvement in the thermal conductivity of the amorphous polyimide ULTEM was achieved. Our study demonstrates that the thermal conductivity coefficient is anisotropic in different directions with respect to the deformation axis and shows a significant increase in both semicrystalline and amorphous PIs in the direction parallel to the deformation. Both types of structural ordering (self-ordering of semicrystalline PI and mechanical elongation) led to the same significant increase in thermal conductivity coefficient.