Free fermions on Hamming graphs $H(d,q)$ are considered and the entanglement entropy for two types of subsystems is computed. For subsets of vertices that form Hamming subgraphs, an analytical expression is obtained. For subsets corresponding to a neighborhood, i.e. to a set of sites at a fixed distance from a reference vertex, a decomposition in irreducible submodules of the Terwilliger algebra of $H(d,q)$ also yields a closed formula for the entanglement entropy. Finally, for subsystems made out of multiple neighborhoods, it is shown how to construct a block-tridiagonal operator which commutes with the entanglement Hamiltonian. It is identified as a BC-Gaudin magnet Hamiltonian in a magnetic field and is diagonalized by the modified algebraic Bethe ansatz.
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