Herein, graphene oxide was used as the highly efficient phenazopyridine adsorbent from aqueous medium, synthetic, and human urine. The nanoadsorbent was characterized by different instrumental techniques. The adsorption capacity (1253.17 mg g−1) was reached at pH 5.0, using an adsorbent dosage of 0.125 g L−1 at 298 K. The Sips and Langmuir described the equilibrium data well. At the same time, the pseudo-second order was more suitable for fitting the kinetic data. Thermodynamic parameters revealed the exothermic nature of adsorption with an increase in randomness at the solid-liquid interface. The magnitude of the enthalpy variation value indicates that the process involves the physisorption phenomenon. At the same time, ab initio molecular dynamics data corroborated with the thermodynamic results, indicating that adsorbent and adsorbate establish hydrogen bonds through the amine groups (adsorbate) and hydroxyl groups on the adsorbent surface (weak interactions). Electrostatic interactions are also involved. Additionally, the adsorption assays conducted in simulated medium and human urine showed the excellent performance of adsorbent material to remove the drug in real concentrations excreted by the kidneys (removal values higher than 60%).