Increasing usage and recent accidents due to Lithium ion (Li-ion) batteries exploding or catching on fire has inspired research on the thermal management of these batteries. In cylindrical 18650 cells, heat generated during the charge/discharge cycle must dissipate to the surrounding through its metallic case due to the poor thermal conductivity of the jelly roll, which is spirally wound with many interfaces between electrodes and the polymeric separator. This work develops a technique to measure the thermal resistance across the case-separator interface, which ultimately limits heat transfer out of the jelly roll. Commercial 18650 batteries are discharged and opened using a battery disassembly tool, and the 25 μm thick separator and the 200 μm thick metallic case are harvested to make samples. A miniaturized version of the conventional reference bar method (ASTM D5470) combined with infrared thermal microscopy to map the temperature profile including the interfacial temperature jumps enables measurement of the interfacial thermal conductance across a range of case temperatures and interface pressures. The mean thermal conductance across the case-separator interface is 670 ± 275 W/(m2 K) and no significant temperature or pressure dependence on is observed.