Prüfer codes provide an encoding scheme for representing a vertex-labeled tree on $n$ vertices with a string of length $n-2$. Indeed, two labeled trees are isomorphic if and only if their Prüfer codes are identical, and this supplies a proof of Cayley's Theorem. Motivated by a graph decomposition of freight networks into a corpus of vertex-colored rooted trees, we extend the notion of Prüfer codes to that setting, i.e., trees without a unique labeling, by defining a canonical label for a vertex-colored rooted tree and incorporating vertex colors into our variation of the Prüfer code. Given a pair of trees, we prove properties of the vertex-colored Prüfer code (abbreviated VCPC) equivalent to (1) isomorphism between a pair of vertex-colored rooted trees, (2) the subtree relationship between vertex-colored rooted trees, and (3) when one vertex-colored rooted tree is isomorphic to a minor of another vertex-colored rooted tree.