The information technology (IT) industry is exploring three-dimensional (3D) stacking of chips to maintain future computing scalability. However, 3D chip stacks require a solution to significant new thermal challenges. Interlayer twophase evaporative cooling with a chip-to-chip interconnectcompatible dielectric fluid is an enabling technology but faces significant development issues. One such issue is the inability to thermally model a microprocessor with spatially varying heat sources together with a two phase microfluidic convection network. While progress has been made on two-phase conjugate simulations at the chip and channel levels, none of those provide a computationally manageable approach. In the present study, a reduced physics conjugate heat transfer model has been developed for simulating two-phase flow boiling through chip embedded micron scale cavities. This model has been validated with good accuracy against data available from literature. The validated model was then extended to predict the thermal performance of a state-of-theart microprocessor chip with embedded two-phase cooling, where significant improvements in device junction temperatures were observed compared to the baseline cooling solution.