Quantum Key Distribution (QKD) is an innovative technology which exploits the laws of quantum physics to generate and distribute shared secret key for use in cryptographic devices. Quantum Key Distribution offers the advantage of ‘unconditionally secure’ key generation with the unique ability to detect eavesdropping on the key distribution channel and shows promise for high-security applications such as those found in banking, government, and military environments. However, Quantum Key Distribution is a nascent technology where realized systems suffer from implementation non-idealities, which may significantly impact system performance and security. In this article, we discuss the modeling of a decoy state enabled Quantum Key Distribution system built to study the impact of these practical limitations. Specifically, we present a thorough background on the decoy state protocol, detailed discussion of the modeled decoy state enabled Quantum Key Distribution system, and evidence for component and sub-system verification, as well as, multiple examples of system-level validation. Additionally, we bring attention to practical considerations associated with implementing the decoy state protocol security condition gained from these research activities.