To resolve the problem of mobile electrolytes for the permeation of hydrogen isotopes in fuel cells, we have studied herein heteronuclear fullerene nanocages (Al12N12, Al12P12, B12N12, and B12P12) for the separation and permeation of hydrogen isotopes. The separation and permeation of fullerene nanocages for hydrogen isotopes are studied at ωB97XD functional of DFT along with 6–31g (d,p) pople basis set. Zero-point energy (ZPE) is calculated for Protium (H+) and its heavier isotopes including deuterium (D+) and tritium (T+). The Arrhenius equation is employed to calculate the selectivity of protium to deuterium (H+/D+) and deuterium to tritium (H+/T+) isotopes. The selectivity is calculated by using the zero-point energy difference (ZPE) of protium (H+) to its heavier isotopes. The proposed fullerene nanocages estimated better selectivity for proton isotopes. The phosphide-based nanocages (Al12P12, B12P12) provide superior selectivity values of H+/D+ and H+/T+ compared to nitrogen-based nanocages (Al12N12, B12N12). This study provides insights into separation pathways for proton isotopes through nanocages for many industrial applications in the energy sector.