Low-valent palladium nanoparticles are efficient species promoting catalytic activity and selectivity in a number of chemical reactions. Recently, an atom-centered cuboctahedral Pd13 motif has been characterized as a ligand-protected [Pd13(Tr)6]2+ cluster featuring a 1S2 superatomic shell structure. In this report, we account for the ligand-cluster and endohedral-cage interaction in [Pd13(Tr)6]2+, which accounts for a favorable situation in the overall cluster. In addition, the spherical aromatic properties are evaluated to understand the behavior of the ligand-protected Pd13 cluster core. Our results denote a sizable interaction towards carbon-based ligands in an overall spherical aromatic cluster featuring a long-range shielding cone. Thus, [Pd13(Tr)6]2+ is rationalized as the first ligand-protected palladium cluster to date featuring spherical aromatic properties, serving as a stable building block for molecular-based materials or as a dopant in porous carbon materials.