The utilization of non-edible/waste oils and microwave heating system are expected to reduce the cost of biodiesel and contribute to reducing global food demand. In this study, the continuous biodiesel production from waste cooking oil (WCO) by the use of a microwave flow system has been investigated. The utilization of WCO as a biodiesel feedstock is expected to minimize the industrial biodiesel production. A household microwave was modified as a biodiesel reactor for continuous transesterification. The effect of transesterification reaction parameters such as methanol/WCO molar ratio (3:1, 6:1 and 9:1), quantity of the catalyst (0.5%, 0.75%, 1% and 1.5%in weight of KOH) and flow rate of reactant (6, 10.5 and 14.5ml/ min) in various microwave output power (360, 450, 540, 630 and 720 watts) on the biodiesel yield has been evaluated. Results showed that WCO can be converted to biodiesel (96.53%) within 4min under methanol/oil molar ratio of 6:1, 0.75 wt. % catalyst, 6ml/min flow rate in 450W microwave output power. Moreover, the results explained that the high yield can be obtained when the reaction temperature is in the range of 40-45 °C. Microwave assisted continuous transesterification process is simple, practical, time-saving and no requirement to pretreatment of feedstock, offering alternative production method to produce biodiesel according to European Union draft standards.