The synthesis of biodiesel or fatty acid methyl esters (FAMEs) from alternative feedstocks such as waste cooking oil through conventional transesterification process is challenged by the presence of significant amounts of free fatty acids (FFAs). Alternatively, these FFAs can also serve as raw material for the synthesis of FAMEs through acid-catalyzed esterification. In this study, we utilized graphene oxide (GO) as a carbon-based heterogeneous acid catalyst in synergy with microwave (MW) heating as a novel approach for an efficient synthesis of FAMEs by esterification reaction at a shorter reaction time. Under this process, 99.2% FAME was achieved at 3 min, methanol/oleic acid molar ratio of 12, MW power of 200 W, and 1 wt % catalyst. It shows excellent catalytic performance, which is more active than Amberlyst 15, sulfated zirconia, and graphite oxide. Among the process variables investigated, the ratio of methanol/oleic acid is the most important factor for higher FAME yield. Additionally, the MW absorbing property of catalyst is necessary for a successful synthesis. Therefore, the synergy of MW and GO is a promising technique for a cost-competitive biodiesel production from low-cost feedstocks containing high free fatty acids.