Biodiesel, an alternative diesel fuel made from renewable sources such as vegetable oils and animal fats, is becoming prominent among alternatives to conventional petro-diesel due to economic, environmental and social factors. Transesterification is the most preferred method of biodiesel production. Knowledge of transesterification reaction kinetic enables prediction of the extent of the chemical reaction at any time under particular conditions. It is also essential in the design of reactors for biodiesel production in industrial scale, determination of kinetic model and optimization of operation conditions. In this study, a mathematical model for the microwave assisted trans-esterification reaction of microalgae and methanol has been developed to study the effect of the operating parameters on the process kinetics. A well-mixed microwave reactor was used to express the laboratory scale microwave reactor at stirring speed 500 rpm. Mass transfer controlled state was assumed to be minimal using the stirring condition. The model developed was based on experimental data described in a previous study. The experimental works were designed to study the effect of reaction time between 1-5 min; power of microwave of 100-400 W, and an amount of CaO catalyst of 1 and 3%. The use of a solid catalyst effectively reduces the purification cost of biodiesel due to ease of separation and potential for reuse. The molar ratio of microalgae oil and methanol was constant at the ratio of 1: 6. The validation of model indicated that the reaction have second order reaction in terms of triglycerides. A very good correlation between model and experiment data was observed by correlation coefficient (R 2) and least square curve fit. In addition, the experiment shows that the best conditions for reaction time were 5 min, power of microwave was 400 W and amount of CaO catalyst was 3%. The maximum yield of biodiesel in the best conditions was 93.23%.