Sulfamethoxazole (SMZ), carbamazepine (CBZ), and ketoprofen (KET) adsorption using graphene oxide (GO) functionalized with ionic liquids (IL) was investigated. Ionic liquid 1-hexyl 3-decahexyl imidazolium was synthesized and characterized using high resolution-mass spectrometry and nuclear magnetic resonance (H-1 and C-13 NMR). GO and GO-IL were synthesized and characterized using thermal gravimetric analysis, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectroscopy, scanning electron microscopy, surface area and porosity analysis, and zeta potentials. Computational, isotherm, kinetics, and regeneration studies were carried out to determine the adsorption capacity, adsorption mechanism, and reusability of the material for the adsorption of SMZ, CBZ, and KET. Density functional theory (DFT) and our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) (quantum mechanics and molecular mechanics) approach were applied to describe the nature of the interaction, energetics, charge distribution, and pH effect during the sorption of the pharmaceutical compounds on the adsorbents at the molecular level. Effects of solution pH, contact time, adsorbent dosage, and energetics on the selected pharmaceuticals were also investigated experimentally. The pH plays a significant role on the adsorption of SMZ and KET but has no significant effect on the adsorption of CBZ on both GO and GO-IL. Pseudo-second-order and Langmuir models best explained the kinetics and adsorption isotherm, respectively. GO-IL showed superior adsorption efficiency for the selected pharmaceuticals when compared to GO.