Stationary phase development for hydrophilic interaction chromatography is rapidly gaining attention due to its versatile application in the separation of diversified solutes. Considering the hydrogen bonding property of urea, we designed and synthesized double‐alkylated L‐lysine derived urea containing short and long chain systems for use as stationary phases in hydrophilic interaction chromatography after immobilizing onto silica. The compounds were characterized by elemental analysis, NMR, and Fourier transform infrared spectroscopy. The compounds were further investigated by thermogravimetric analysis and diffuse reflectance infrared Fourier transform spectroscopy after immobilization onto silica. The effect of chain length in hydrophilic interaction chromatography, the phases were used for the separation of nucleic acid bases, nucleosides, and sulfa drugs. Enhanced selectivity was observed for both phases. However, the L‐lysine‐derived urea‐containing phase with short alkyl chains showed better separation ability than did the phase with longer alkyl chains. The former also showed better performance in terms of other chromatographic parameters such as efficiency, resolution, and asymmetry as compared to the latter.