In this study, the transesterification of waste cooking oil and methanol aimed to produce biodiesel and use of KOH/Clinoptilolite as a heterogeneous catalyst in the microreactor as a new reactor to accelerate this process. Therefore, a semi-industrial pilot was investigated under different conditions for biodiesel production and optimizing the operating conditions. In order to optimize these conditions, the effect of important factors was studied including reaction temperature, catalyst concentration, volume ratio of oil-to-methanol and residence time on the purity of biodiesel produced through response surface methodology (RSM). After data analysis and optimizing the reaction of biodiesel production, the highest purity of produced biodiesel was obtained at reaction temperature of 65 °C, catalyst concentration of 8.1 wt%, oil/methanol volume ratio of 2.25:1 and residence time of 13.4 min which resulted in a biodiesel production with a purity of 97.45%. Based on the results, the use of microchannel can reduce the reaction time by the increase of mixing. Further, the cost of biodiesel production can be reduced using waste cooking oil and KOH/Clinoptilolite.