The three different regioisomers of bis-N-methylfulleropyrrolidines have been separated by controlling the relative amounts of γ-cyclodextrin and dimethyl sulfoxide (DMSO) contained in solutions of these compounds. When a small amount of γ-CDx was used in a mechanochemical high-speed vibration milling apparatus, the trans-1 and trans-2•γ-CDx complexes were separated from the trans-3•γ-CDx complex. In contrast, trans-3 was extracted in a relatively high ratio with an excess of γ-CDx. The addition of DMSO to aqueous solutions of the fullerene derivative•γ-CDx complexes allowed for the three regioisomers to be obtained in high purity (>95%). The basis for the observed regioselective separation was a competition between the relative stabilities and solubilities of the complexes in the water and water-DMSO solvents. The stabilities of the complexes in water were assessed by the number of hydrogen bonding interactions between the two γ-CDx units using molecular dynamics simulations. To the best of our knowledge, this is the first reported example of the isolation of the different regioisomers of fullerene derivatives using host-guest complexes.