A new chemically modified electrode has been constructed based on Lysine modified carbon paste electrode (LCPE). The electrode was evaluated as sensor for sub-micromolar determination of vanillin. LCPE displayed excellent electrochemical catalytic activity towards vanillin. The oxidation peak of vanillin increased significantly compared to that of carbon paste electrode (CPE). The electrochemical behavior of vanillin at the surface of LCPE has been analyzed with respect to sweep rate and pH of the solution. An analytical procedure based on differential pulse voltammetry (DPV) has been optimized with a detection limit of 2.88 μM (S/N = 3). The proposed method has been successfully applied for the determination of vanillin in real samples, and the assay results were satisfactory.