An electrochemical sensor‐based on nickel selenide quantum dot, capped with 3‐mercaptopropionic acid (3‐MPA), was embedded on an L‐cysteine modified gold electrode for nevirapine (NVP) detection. The 3‐MPA‐NiSe2QD material was fully characterised using FTIR, SEM, Raman, HR‐TEM, XRD, SAXS, PL and UV‐Vis. Differential pulse voltammetry was used to study the electrochemical responses of 3‐MPA‐NiSe2QD/L‐cyst/Au electrochemical sensor to NVP, with a characteristic oxidation peak at 0.76 V. The electrochemical sensor obtained a low limit of detection (LOD) value of 0.0133 pM (0.0035 ng/L), limit of quantification (LOQ) of 0.0442 pM (0.0118 ng/L) and sensitivity of 6.15 μA/pM with a linear range of 0.25–0.63 pM, respectively. Thus, the reproducibility, stability, and repetitive usability shown by the proposed sensor made it suitable for the determination of nevirapine in real wastewater samples.