Glycerol is a major byproduct obtained in the production of biodiesel, an important renewable fuel. The presence of free glycerol in fuel can have structural and performance consequences with respect to the engine, making fuel quality control important. The standard method to analyze glycerol in biodiesel is gas chromatography, a time-consuming and expensive technique. In this context, an electrode based on glassy carbon electrodes (GCEs) modified with reduced graphene oxide and core-shell gold@palladium nanoparticles was developed for the determination of glycerol in biodiesel. The free glycerol analysis was performed in the aqueous phase obtained by liquid–liquid extraction from a biodiesel sample. Cyclic voltammetry was chosen as the method for glycerol electrochemical analysis to regenerate active sites and promote greater sensor stability. The modified Au@Pd/rGO/GCE electrode showed an excellent performance, obtaining a linear range of 18.2 to 109 µmol L−1 with a correlation coefficient of 0.9895, limits of detection and quantification of 5.33 and 17.6 µmol L−1, respectively, high stability during 1000 cycles, and recovery values of 86% and 87% in the quantification of glycerol in biodiesel samples. The proposed method proved to be a great alternative for the analysis of glycerol in biodiesel, being a fast, sensitive, and low-cost technique due to its high stability and the use of small quantities of reagents.