In biodiesel industries, the removal of glycerol from biodiesel is very important in the downstream process of the biodiesel production since the presence of glycerol in biodiesel causes diesel engine problems. Glycerol is commonly separated from biodiesel by extraction method using water, however, this method results in a vast amount of wastewater and requires a high energy consumption. In this work, a ceramic microfiltration membrane made of α-alumina was applied to remove glycerol from biodiesel. The microfiltration experiment was carried out using biodiesel containing various glycerol concentrations as the feed. For all investigated glycerol concentrations from 1000 ppm until 10,000 ppm in the feed, the membrane showed an excellent separation performance with rejection values of 91 to 99%. The profile of the permeate flux against the permeation time showed a flux decline because of the fouling phenomenon during the crossflow microfiltration experiment, and stable permeate fluxes were obtained after 2 h of permeation time. The result of this work showed that the separation process using the microfiltration membrane is a promising method to purify biodiesel instead of the conventional water washing method.