The purpose of the present study is to produce biodiesel from fish-waste oil and methanol by combining mechanical stirring and microwave as a technique to accelerate this process. In this research, a microwave system was used including microwave source, stirrer, spiral tube and decanter. With the help of this system, the effects of multiple parameters on the conversion of fatty acid to methyl ester is investigated. These parameters include molar ratio of alcohol to oil (4 to 1, 6 to 1 and 8 to 1), catalyst concentration (0.5, 1 and 1.5 weight percent of oil), reaction time (5, 15 and 25 min) and microwave time (0.5, 1.5 and 2.5 min). Analyzing the obtained results is performed using the response surface method and Box Behnken layout in Design Expert 10.0 software. After analyzing the data and optimizing the biodiesel production reaction, the highest percentage of biodiesel conversion (92.62%) was found in the catalyst concentration of 1.13%, the reaction time of 24.61 minutes, the molar ratio of alcohol to oil of 5.55 and the microwave time of 0.5 minute. The regression model between independent variables and dependent variable (percent conversion) was obtained as a quadratic equation with R2=0.9953.