Waste cooking oil (WCO) can be an alternative feedstock for biodiesel production. However, very often WCO containing high free fatty acid (FFA) with value above 3% that can reduce the quality and quantity of the biodiesel production is not suitable for direct alkali base transesterification. This research deployed glycerolysis reaction to reduce the FFA of WCO prior to transesterification reaction. Previous works on glycerolysis have reported that glycerolysis reaction required high temperature, longer reaction of time and high energy intense. This research paper reports improved glycerolysis reaction to effectively reduce FFA in WCO using continuous flow microwave irradiation. Initially, the experiment was conducted manually to determine the suitable microwave power for the reaction and found 440W microwave power able to reduce the FFA value the most. Subsequently, response surface methodology (RSM) has been used with three operating variables, namely molar ratio of oil to glycerol, pump speed and reaction time with a total of 17 experiment runs to determine the overall optimum parameters for microwave assisted glycerolysis of WCO. From this study, under the ideal conditions of 1:1 w/w oil to glycerol ratio, 70 rpm pump speed and 10 minutes reaction time, the FFA value has reduced from 3.95% to 0.34%.