In our current investigation, we employed a B12N12 nanocage to extract paracetamol from water utilizing a DFT approach. We explored three distinct positions of paracetamol concerning its interaction with the B12N12 nanocage, designated as complex-1 (BNP-1), complex-2 (BNP-2), and complex-3 (BNP-3), under both aqueous and gaseous conditions. The optimized bond distances exhibited strong interactions between the nanocage and the paracetamol drug in BNP-1 and BNP-3. Notably, BNP-1 and BNP-3 displayed substantial chemisorption energies, measuring at −27.94 and −15.31 kcal/mol in the gas phase and −30.69 and −15.60 kcal/mol in the aqueous medium, respectively. In contrast, BNP-2 displayed a physiosorbed nature, indicating weaker interactions with values of −6.97 kcal/mol in the gas phase and −4.98 kcal/mol in the aqueous medium. Our analysis of charge transfer revealed significant charge transfer between the B12N12 nanocage and paracetamol. Additionally, a Quantum Theory of Atoms in Molecules (QTAIM) analysis confirmed that the O─B bond within BNP-1 and BNP-3 exhibited a strong covalent and partial bond, encompassing both covalent and electrostatic interactions. In contrast, the H─N bond within BNP-2 displayed a weaker hydrogen bond. Further investigation through Noncovalent Interaction (NCI) and Reduced Density Gradient (RDG) analyses reinforced the presence of strong interactions in BNP-1 and BNP-3, while indicating weaker interactions in BNP-2. The decrease in the electronic band gap (Eg) demonstrated the potential of B12N12 as a promising adsorbent for paracetamol. Examining thermodynamics, the negative values of ∆H (enthalpy change) and ∆G (Gibbs free energy change) pointed out the exothermic and spontaneous nature of the adsorption process. Overall, our study underscores the potential of B12N12 as an effective adsorbent for eliminating paracetamol from wastewater.