The analytical form of the perturbation theory for the MC SCF method of Veillard and Clementi is presented. The appropriate second-order energy functional which takes into account the self-consistency requirements, leads to a set of coupled first-order perturbed equations determining the perturbed configuration coefficients and orbitals. The second-order energy formula derived from this functional can be given a clear physical interpretation. The present analytical approach is compared with the finite perturbation MC SCF scheme.