A thick-restart Lanczos type algorithm is proposed for Hermitian $J$-symmetric matrices. Since Hermitian $J$-symmetric matrices possess doubly degenerate spectra or doubly multiple eigenvalues with a simple relation between the degenerate eigenvectors, we can improve the convergence of the Lanczos algorithm by restricting the search space of the Krylov subspace to that spanned by one of each pair of the degenerate eigenvector pairs. We show that the Lanczos iteration is compatible with the $J$-symmetry, so that the subspace can be split into two subspaces that are orthogonal to each other. The proposed algorithm searches for eigenvectors in one of the two subspaces without the multiplicity. The other eigenvectors paired to them can be easily reconstructed with the simple relation from the $J$-symmetry. We test our algorithm on randomly generated small dense matrices and a sparse large matrix originating from a quantum field theory.