We demonstrate that non-Hermitian Hamiltonian systems with spontaneously broken PT-symmetry and partially complex eigenvalue spectrum can be made meaningful in a quantum mechanical sense when introducing some explicit time-dependence into their parameters. Exploiting the fact that explicitly time-dependent non-Hermitian Hamiltonians are unobservable and not identical to the energy operators in such a scenario, we show that their corresponding non-Hermitian energy operators develop a different type of PT-symmetry from the Hamiltonians that ensures the reality of their energy spectra. For this purpose we analytically solve the fully time-dependent Dyson equation with all quantities involved being explicitly time-dependent giving rise to a time-dependent metric. The key auxiliary equation to be solved for the two level atomic system considered here is the nonlinear Ermakov–Pinney equation with time-dependent coefficients.