Given the scarceness of fossil fuels and high volume of pollution caused through the consumption of these fuels, many efforts are being made to produce alternative fuels. Biodiesel is one of the alternatives to diesel fuels. The main problem with biodiesel production is higher operation costs, as compared with diesel fuels. In this study, waste cooking oil and cow bone as the catalyst were used to reduce feed costs as much as possible. Moreover, a microreactor was utilized to reduce the residence time to 1 min. Using Box-Behnken design method, the effect of different variables including catalyst concentration (calcined cow bone), oil to methanol volume ratio, residence time, and reaction temperature on the purity of produced biodiesel were examined. The results showed that when using a catalyst concentration of 8.5 wt %, an oil to methanol volume ratio of 2.25 vol: vol, a residence time of 60 s, and a temperature of 63.1 °C, the maximum purity of biodiesel was 99.24%.