Molecular dynamics (MD) simulations over a 30 ns trajectory have been carried out on apoflavodoxin from Azotobacter vinelandii to compare with the published, experimental time-resolved fluorescence anisotropy results of Förster Resonance Energy Transfer (FRET) between the three tryptophan residues. MD analysis of atomic coordinates yielding both the time course of geometric parameters and the time-correlated second-order Legendre polynomial functions reflects immobilization of tryptophans in the protein matrix. However, one tryptophan residue (Trp167) undergoes flip-flop motion on the nanosecond timescale. The simulated time-resolved fluorescence anisotropy of tryptophan residues in apoflavodoxin implying a model of two unidirectional FRET pathways is in very good agreement with the experimental time-resolved fluorescence anisotropy, although the less efficient FRET pathway cannot be resolved and is hidden in the contribution of a slow protein motion.