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Quantum Key Distribution (QKD) is an emerging technology which uses the principles of quantum mechanics to provide unconditionally secure key distribution. QKD systems are unique in their ability to detect an eavesdropper's presence and are being marketed for applications where high levels of secrecy are required such as banking, government, and military environments. QKD systems are composed of electrical, optical, and electrooptical components. Their design requires expertise across multiple disciplines including computer science, computer engineering, electrical engineering, information theory, optical physics, and quantum physics. This multidisciplinary nature makes QKD an ideal candidate for study using Model Based Systems Engineering (MBSE) Processes, Methods, and Tools (PMTs). The primary research goal is to gain understanding of the operation and performance of the QKD decoy state protocol through the use of MBSE PMTs. The main research contributions include development of a decoy state model, validation of the this protocol in a QKD system model implementation, and confirmation that application of MBSE PMTs are critical to the understanding and analysis of complex systems. This work presents the first known application of MBSE PMTs to analyze a QKD system and provides utility to system developers, designers and analysts who seek to quantify performance and security.