We propose a novel method using a quantum annealer -- an analog quantum computer based on the principles of quantum adiabatic evolution -- to solve the Graph Isomorphism problem, in which one has to determine whether two graphs are isomorphic (i.e., can be transformed into each other simply by a relabeling of the vertices). We demonstrate the capabilities of the method by analyzing several types of graph families, focusing on graphs with particularly high symmetry called strongly regular graphs (SRG's). We also show that our method is applicable, within certain limitations, to currently available quantum hardware such as "D-Wave One".