A procedure is described that can be used to reconstruct the quantum state of a molecular ensemble from time-dependent internuclear probability density functions determined by time-resolved electron diffraction. The procedure makes use of established techniques for evaluating the density matrix and the phase-space joint probability density, that is, the Wigner function. A novel expression for describing electron diffraction intensities in terms of the Wigner function is presented. An approximate variant of the method, neglecting the off-diagonal elements of the density matrix, was tested by analyzing gas electron diffraction data for N2 in a Boltzmann distribution and TRED data obtained from the 193 nm photodissociation of CS2 to carbon monosulfide, CS, at 20, 40, and 120 ns after irradiation. The coherent changes in the nuclear subsystem by time-resolved electron diffraction method determine the fundamental transition from the standard kinetics to the dynamics of the phase trajectory of the molecule and the tomography of molecular quantum state.