This work details the theory and implementation of a multi-wavelength quantum key distribution (QKD) emulation system with a physical unclonable function (PUF). Multi-wavelength QKD can eliminate the need to share a subsection of the final key for eavesdropper detection and allow for ternary and quaternary data transmission. The inclusion of the PUF adds an additional layer of security. We provide preliminary error analysis of our emulation system. To support this work, we introduce a bitwise transform operator that enables binary output of the PUF to satisfy the ternary and quaternary input requirements of the QKD system.