Structural flexibility has become a common feature in emerging microsystems with increasing heat fluxes. The thermal control of such applications is a significant challenge because of both structural and volumetric requirements, where standard cooling solutions are not applicable. Flexible polymer microlayers are a promising solution for the embedded cooling of such microsystems. In the present investigation, a flexible polydimethylsiloxane (PDMS) microgap is proposed and assessed in an effort to prove its viability for thermal management in the aforementioned applications. The analyzed polymer microgap features a dedicated vapor pathway design which is proven to assist in the efficient removal of vapor from the microsystem. The dielectric refrigerant HFE-7100 is used as the working fluid under flow boiling conditions, reporting on the two-phase flow regime, heat transfer, and pressure drop. In addition to experimental results, the numerical modeling of the relevant features of flow boiling is explored with the use of a mechanistic phase-change model that is proven to accurately predict the flow variables and constitutes a valuable tool in the analysis and design of such microsystems. The results from this study demonstrate that this approach is feasible for the removal of relatively high heat fluxes which are comparable to metallic-based or silicon microchannels, with the added advantage of structural flexibility while also providing a stable two-phase cooling mechanism.