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Biodiesel produced from waste cooking oils (WCOs) mixed with methanol was efficiently transesterified using a continuous fluid flow system with a focused microwave heating device. Strontium oxide (SrO) was added as the catalyst. The factors that most influence the biodiesel conversion rate were first estimated by considering the effects of oil-to-methanol ratio, added quantity of SrO, and microwave heating power on reaction time in a built-in batch unit. The optimal parameter values were then applied to a continuous fluid flow system, which simulates the conversion of a scaled-up quantity of WCOs into biodiesel. Under the optimum fluid flow velocity and an appropriate output temperature, a biodiesel conversion rate of ca. 93 % was reached, associated with the decomposition of ester bonds and the formation of a tetrahedral intermediate substance during the reaction.