The adsorption of penicillamine (PCA) on pure B12N12 and B12CaN12 nanocages in aqueous and chloroform solvents has been evaluated using density functional theory (DFT) calculations. The interaction of PCA on B12N12 nanocages is chemisorption through its four nucleophilic sites: amine, carbonyl, hydroxyl and thiol. The most stable adsorption configuration was achieved when zwitterionic PCA adsorbs via its carbonyl group in water with value of −1.723 eV, in contrast, when neutral PCA adsorbs via its amine group in chloroform with value of −1.68 eV. Intercalated calcium ion within B12N12 nanocage (B12CaN12) was shown to attract PCA onto nanocage surface, resulting in higher solubility and adsorption energy after their complexation in water and chloroform. The adsorption of multiple PCA molecules from their amine and carbonyl groups on pure and B12CaN12 nanocages were also evaluated where two and three molecules can be chemisorbed on boron atoms of the nanocage surfaces with the adsorption energy per PCA reduces slightly with the increasing the amount of drugs due to the curvature effects. Molecular docking study indicates that PCA from its NH2 group on B12CaN12 nanocage has the best binding affinity and inhibition potential of tumor necrosis factor-alpha (TNF-α) and Interleukin-1 (IL-1) receptors as compared with the other adsorption systems. Molecular docking and ADMET analysis displayed that the chosen compounds pass Lipinski Rule and have appropriate pharmacokinetic features suitable as models for developing anti-inflammatory agents.