This experimental study aimed to evaluate nitrate removal from a fine-grained soil using electrokinetic (EK) technique coupled with granular activated carbon-permeable reactive barrier (GAC–PRB). Besides, a model was developed to optimize the operational parameters for a given soil with different levels of contamination. After determination of equilibrium time, 16 batch experiments were conducted to investigate adsorbent properties comprising equilibrium time, optimum adsorbent dosage, the effect of initial concentration, and stirring speed. The isotherm data were correlated to various isotherm models, and kinetic data suitably followed the pseudo-second-order model. By employing a central composite design, the impact of initial nitrate concentration (28–472 mg/l), voltage gradient (0.8–2.2 V/Cm), and remediation time (2.5–5.5 day) on EK/GAC–PRB removal efficiency and energy consumption were investigated. Also, response surface method was further employed for modelling, optimizing and interpreting the responses. Results showed that EK assisted by GAC–PRB could efficiently remove nitrate from a fine-grained soil up to 96%. Perturbation plots indicated voltage gradient, and remediation time had the most effect on nitrate removal efficiency and energy consumption. Furthermore, it was found that for a given soil spiked with 275 mg/l nitrate, the model proposes 5.5-day remediation and 1 V/cm to maximize removal efficiency and to minimize energy consumption. It was identified that electromigration was the primary mechanism of nitrate transportation in the process by analysing nitrate content along the soil chamber. Finally, the removal of nitrate in the system was proved by using scanning electron microscopy analysis.