Heat conduction through bonded metal-polymer interfaces often limits the overall heat transfer in electronic packaging, batteries, and heat recovery systems. To design the thermal circuit in such systems, it is essential to measure the thermal interfacial resistance (TIR) across ∼1 µm to 100 µm junctions. Previously reported TIR of metal-polymer junctions utilize ASTM E1530-based two-block systems that measure the TIR by applying pressure across the interface through external heating and cooling blocks. Here, we report a novel modification of the ASTM-E1530 technique that employs integrated heaters and sensors to provide an intrinsic TIR measurement of an adhesively bonded metal-polymer junction. We design the measurement technique using finite element simulations to either passively suppress or actively compensate the lateral heat diffusion through the polymer, which can minimize the systematic error to ≲5%. Through proof-of-concept experiments, we report the TIR of metal-polymer interfaces made from DuPont's Pyralux double-side copper-clad laminates, commonly used in flexible printed circuit boards. Our TIR measurement errors are <10%. We highlight additional sources of errors due to non-idealities in the experiment and discuss possible ways to overcome them. Our measurement technique is also applicable to interfaces that are electrically insulating such as adhesively joined metal-metal junctions and sputter-coated or welded metal-polymer junctions. Overall, the technique is capable of measuring TIR ≳10-5 m2 KW-1 in bonded metal-polymer foils and can be tailored for in situ measurements in flexible electronics, circuit packaging, and other hybrid metal-polymer systems.