In this paper, the entanglement entropy is investigated in the ground state of a spinless free fermion Hamiltonian where its hopping matrix is given by the adjacency matrix of the graph. The bipartite entanglement entropy is calculated from the eigenvalues of the correlation matrix. The entanglement entropy and mutual information are calculated for some scalable graphs including a complete graph and three sets of strongly regular graphs (SRGs). In addition, the volume law scaling has been shown for these graphs. Then, we use the entanglement entropy as a tool for studying the graph isomorphism problem in some non-isomorphic pairs of graphs in order to distinguish them from each other. Two graphs are isomorphic when they are related to each other by relabeling the graph vertices. We study the graph isomorphism in non-isomorphic SRGs, distance-regular graphs and pseudo distance-regular graphs. Most pairs of non-isomorphic SRGs can be distinguished from each other by using fermionic entanglement entropy.