Protonated water clusters confined to the carbon nanotube (CNT) channels of sub-nanometer diameter is beyond the realm of a continuum description. The stericcompulsions offered by the narrow geometry can restrict the formation of hydrogen bond between the water molecules but enhance water and channel interactions. Herein, we have made an attempt to investigate the factors, which are strongly affecting the structure and energy barrier for proton transfer in Zundel cation under the confinement of CNT by employing dispersion-corrected density functional theory-based methods. Our results reveal that the diverse nature of water–water and water–wall interaction inside the nanotube for different size of CNT channels can have remarkable effects on the energetics of the proton transfer process, geometrical parameters, oscillatory shuttling motion of the proton and various energy components, viz. interaction energy, hydrogen bond energy, etc. due to these factors, the proton oscillation in Zundel cation is shown to be nonmonotonic in nature with respect to the conclusions can have important implications and motivate further investigations to understand the fluidics under confined nanomaterials. degree of confinement. Finally, we have demonstrated that the effect of confinement rendered by CNT(6,6) on Zundel cation can be the best suitable candidate among the series of CNTs considered in the present study, for assisting the proton transfer in the Zundel cation easily. These conclusions can have important implications and motivate further investigations to understand the fluidics under confined nanomaterials.