A new graphene oxide-based liquid chromatography stationary phase was synthesized, characterized, and used for the first time in the separation of paracetamol and caffeine in pharmaceutical preparations under reversed phase conditions. For this purpose, graphene oxide was synthesized using the modified Hummers method, and Si-GO stationary phase was obtained by immobilizing graphene oxide on aminopropyl silica. The obtained graphene oxide, Si–GO and aminopropyl silica materials were characterized by XRD, SEM, TEM and FTIR analysis. Different mobile phases were used to separate drug molecules in order to determine the mechanism of interaction between drug molecules and the stationary phase. Once the appropriate solvent system was determined, optimum chromatographic parameters such as mobile phase composition (methanol percentage in water), flow rate and column temperature were determined. The linearity of the method was in the range of 0.989–0.997. The maximum relative standard deviation (% RSD) value was calculated as 0.54. Mean recoveries for paracetamol and caffeine were 98%–99%, respectively, and LOD and LOQ were 6 × 10−3 to 6.5 × 10−3 mg/L and 2 × 10−2 to 2.2 × 10−2 mg/L, respectively. The results showed that the new graphene oxide-based stationary phase could be used for the separation of paracetamol and caffeine in pharmaceutical preparations.