The properties of protonated water systems in nano-confinement differ significantly from its bulk counterparts mainly due to the geometric constraint and nature of water–medium interactions. Herein, we have investigated the structure, vibrational spectra and proton transfer energetics of Zundel cation (ZC) under the confinement of boron–nitride nanotubes (BNNTs) by varying the degree of confinement in a systematic manner. Our results based on dispersion-corrected density functional theory (DFT) based methods reveal that the structure of ZC is significantly modified under the confinement and the nature of interaction largely depends on the diameter of BNNT. The ZC effectively forms hydrogen bonds through H_water^...N_BNNT with BNNT. Among the BNNTs considered in the present study, the maximum interaction energy of ZC and minimum energy barrier for proton transfer are observed for the case of BNNT(5,5). This implies that this particular nanotube can facilitate the proton to easily hop between water molecules of a confined protonated water system.