The excited state of flavin adenine dinucleotide (FAD), dissolved in water, is subjected to intensive quenching due to electron transfer from the adenine moiety to the excited isoalloxazine ring. Increasing the methanol concentration in the solution enhances the quantum yield of the fluorescence. In the present study, we carried out molecular dynamics simulations of FAD in explicit water and water - methanol mixtures over time frames of hundreds of nanoseconds. The simulations record rapid structural fluctuations of the molecule, where the distance between the centers of mass (COMs) of the two nucleotides varied from contact distance (folded) up to fully extended (open) structure. The methanol affected the dynamics of the FAD by enhancing the frequency of unfolding events without any effect on the lifetime of the open state. The correlation of the molecular dynamics simulations with fluorescence titration of the FAD in water/methanol mixtures indicates that the internal quenching takes place when the distance between COMs is <5.5 ± 0.5 Å.