Tautomerization of purine in the water cluster was investigated by the use of DFT calculations. The correlation between the reaction paths and the number of water molecules (n) was examined. For n = 3 and n = 4, concerted reaction paths were obtained. However, for n = 5, a stepwise path including an ion pair intermediate was found with small activation energies. The n = 4 + 3 and n = 4 + 3 + 9 models were calculated to give further small activation energies, where n = 4 constitutes the reaction center and +3 and +3 + 9 denote the number of catalytic water molecules. The combination of the in-plane deprotonation at the N9 site and the out-of-plane protonation at the N7 site makes the n = 4 model probable. Three protonated n = 4 + 3 + 9 routes, a, b, and c, composed of purineH(+)(H2O)(4+3+9) were investigated. The n = 4 + 3 moiety is also included in the three routes, and the route c (with the N1 protonation) was found to be most favorable. The purine tautomerization was found to involve the Zundel cation in the ion pair intermediate.