Intellectual property (IP) core reuse is a common practice for accelerating new product development in modern system-on-chip (SoC) architectures. However, reusing and sharing IP cores in today’s competitive market poses significant security risks. IP watermarking is a potential solution for detecting unauthorized IP duplication and overuse. In this paper, we propose GEM-Water, a robust IP watermark verification scheme that uses electromagnetic (EM) radiation of an IP in an SoC for watermark extraction during boot-up. This is accomplished by applying an n-bit challenge to the IP that triggers some certain state transition in a Finite State Machine (FSM) during boot-up. The FSM output is then mapped into an EM signature which can be extracted and processed to generate expected responses to prove IP ownership. GEM-Water has been implemented in a wide variety of benchmarks using several AMD Xilinx 7 series FPGAs, and the experimental results validate the robustness and viability of the suggested approach with >95% accuracy.