The increasing demand for energy storage materials has gained considerable attention of scientific community toward the development of hydrogen storage materials. Hydrogen has become more important, as it not only works efficiently in different processes but is also used as an alternative energy resource whenever it is combined with a cell technology like fuel cell. Herein, efforts are being made to develop efficient hydrogen storage materials based on alkaline earth metal (beryllium, magnesium, and calcium)-encapsulated B12N12 nanocages. Quantum chemical calculations were performed using density functional theory (DFT) and time-dependent DFT at B3LYP/6-31G(d,p) and CAM-B3LYP/6-311+G(d,p) levels of theory for all the studied systems. The adsorption energies of Be-B12N12, Mg-B12N12, and Ca-B12N12 systems suggested that Mg and Ca are not fitted accurately in the cavity of nanocages because of their large size. However, H2 adsorbed efficiently on the metal-encapsulated systems with high adsorption energy values. Furthermore, dipole moment and QNBO (Charges-Natural Bond Orbital) calculations suggested that a greater charge separation is seen in H2-adsorbed metal-encapsulated systems. The molecular electrostatic potential analysis also unveiled the different charge sites in the studied systems and also demonstrated the charge separation upon hydrogen adsorption on metal-encapsulated systems. Partial density of states analysis was performed in the support of frontier molecular orbital distribution that indicates the narrow highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap in hydrogen-adsorbed metal-encapsulated systems. Results of all analyses and global descriptions of reactivity suggested that the designed H2-adsorbed metal-encapsulated B12N12 systems are efficient systems for designing future hydrogen storage materials. Thus, these novel kinds of systems for efficient hydrogen storage purposes have been recommended.