Quantum technologies, leveraging the principles of quantum mechanics, are rapidly advancing and offer trans-formative benefits in secure communication, computation, and sensing. While quantum communication systems provide unprecedented data security, the implementation security of quantum communication protocols still needs investigation. In this regard, the security of Quantum Key Distribution (QKD) is well studied, while there is limited research on quantum communication protocols beyond QKD. In this work, we study time-delay attacks on generic entanglement distribution quantum communication networks. These networks rely heavily on precise time synchronization between detection stations and a preset coincidence window for accurate identification of distributed entangled pairs. An eavesdropper can exploit this reliance on correct photon arrival timing by introducing a time delay, causing genuine entangled pairs to fall outside the coincidence window. This leads to missed detections, potential false pair identifications, or denial-of-service (DoS) conditions. To mitigate this vulnerability, we propose photon arrival-time monitoring and threshold-based time-delay detection, enabling adaptive coincidence window adjustment. By dynamically centering the coincidence window on the mean photon arrival time, valid entangled pairs can still be accurately identified, even in the presence of a time-delay attack. We simulate the quantum measurement process under different time-delay insertion values in the quantum channel, assuming perfectly synchronized remote detection stations. Our results show the impact of time-delay attacks on entangled pair detection rates, detection accuracy, and fidelity of the reconstructed Bell state. The effectiveness of our proposed countermeasure is demonstrated in simulation, showing that it maintains both the photon count rate and the fidelity at high levels, even when an eavesdropper introduces time delays in the quantum channel.