Studying non-adiabatic effects in molecular dynamics simulations and modeling their optical signatures in linear and non-linear spec-troscopies calls for electronic structure calculations in a situation when the ground state is degenerate or almost degenerate. Such degen-eracy causes serious problems in invoking single Slater determinant Hartree–Fock (HF) and density functional theory (DFT) methods. To resolve this problem, we develop a generalization of time-dependent (dynamical) variational approach which accounts for the degen-erate or almost degenerate ground state structure. Specifically, we propose a ground state ansatz for the subspace of generalized elec-tronic configurations spanned on the degenerate grounds state multi-electron wavefunctions. Further employing the invariant form of Hamilton dynamics we arrive with the classical equations of motion describing the time-evolution of this subspace in the vicinity of the stationary point. The developed approach can be used for accurate calculations of molecular excited states and electronic spectra in the degenerate case.