The protocol evaluation is an integral part of network protocol design. From the perspective of experimental design, discrete event simulations constitute a middle ground between analytical protocol evaluation and testbeds. They allow precise control of otherwise external influences while supporting more detailed protocol models than analytical evaluations. Compared to testbeds, a major restriction is that existing protocols require a separate implementation in the discrete event model. Creating this implementation model may cause differences between the protocol’s simulator-based model and the native implementation, invalidating simulation results. We propose a novel architecture to evaluate unmodified, binary protocol implementations in the state-of-the-art discrete event simulators by utilizing the operating system’s system call barrier. Notably, our approach does not affect discrete simulation properties, such as repeatability, and it does not require the native protocol implementation’s source code. The evaluation results using existing network protocols show the feasibility of our approach in combination with the ns-3 simulator core. We show that our approach more closely resembles realistic protocol performance when compared to simulator-based protocol models. Moreover, our approach performs better than existing solutions for more realistic protocol simulations.