Waste cooking oil (WCO) has attracted attention as a non-edible feedstock for biodiesel. Although an alkali catalyst has several advantages over an acid catalyst in biodiesel production, biodiesel conversion from WCO is only 5.2% when using an alkali catalyst (NaOH), owing to its high free fatty acid (FFA) content of 4.2%. In this study, a novel two-step process in a single reactor, comprised of re-esterification of the FFAs with crude glycerol, using a Tin (II) chloride (SnCl2) catalyst, and subsequent transesterification with methanol, using an alkali catalyst, was adopted, and each step was optimized. This study revealed that the FFA content after re-esterification should be approximately 1.5%, not only to save glycerol and the catalyst involved in the re-esterification, but also to achieve high biodiesel conversion during the transesterification. An alkaline catalyst was successfully used to produce biodiesel in the second step, and a 92.8% conversion to biodiesel was achieved under the optimized conditions (0.6% catalyst relative to WCO, 0.2mL-methanol/WCO, 70ºC, 3 h). Overall, this novel two-step process achieved highly enhanced biodiesel conversion (4.0% to 92.8%) with significantly reduced reaction time (12 h to 4 h) and methanol requirements (15 mL/g-WCO to 0.2 mL/g-WCO).