Quantum communication brings radically new capabilities that are provably impossible to attain in any classical network. Here, we take the first step from a physics experiment to a quantum internet system. We propose a functional allocation of a quantum network stack, and construct the first physical and link layer protocols that turn ad-hoc physics experiments producing heralded entanglement between quantum processors into a well-defined and robust service. This lays the groundwork for designing and implementing scalable control and application protocols in platform-independent software. To design our protocol, we identify use cases, as well as fundamental and technological design considerations of quantum network hardware, illustrated by considering the state-of-the-art quantum processor platform available to us (Nitrogen-Vacancy (NV) centers in diamond). Using a purpose built discrete-event simulator for quantum networks, we examine the robustness and performance of our protocol using extensive simulations on a supercomputing cluster. We perform a full implementation of our protocol in our simulator, where we successfully validate the physical simulation model against data gathered from the NV hardware. We first observe that our protocol is robust even in a regime of exaggerated losses of classical control messages with only little impact on the performance of the system. We proceed to study the performance of our protocols for 169 distinct simulation scenarios, including trade-offs between traditional performance metrics such as throughput, and the quality of entanglement. Finally, we initiate the study of quantum network scheduling strategies to optimize protocol performance for different use cases.