A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the ‘nonempirically tuned range-separated’ density functional is presented. It takes account of the self-consistent orbital relaxation induced by environmental Coulomb field and the exchange interaction in fragment pairs at low computational scaling along the system size. The accuracy was confirmed numerically on benchmark systems of imidazole and furane homo-dimer cations. Applications to hole transfers in DNA nucleobase pairs and in a π-stack adenine octomer highlight the effects of orbital relaxation.