This research evaluates refining waste cooking oil with active natural zeolite, utilizes it for biodiesel synthesis, and characterizes the synthesized methyl ester. This experimental laboratory research was carried out: (1) activation of natural zeolite, (2) refining waste cooking oil with active natural zeolite, (3) determination of free fatty acid (FFA) content of the oil, (4) transesterification with KOH catalyst, (5) characterization of the synthesized methyl esters according to the SNI 7182:2015, and (6) identification of the methyl ester component by GC-MS. The results showed that the FFA content of the refined waste cooking oil using active natural zeolite with concentrations of 10%, 20%, and 30% per mass of oil were 2.97, 2.0, and 1.56%, respectively. The yield of methyl ester transesterified with various concentrations of KOH (0.8, 1.0, and 2% per mass of oil), respectively, were 80.13, 85.34, and 74.98%. The synthesized methyl ester resulted in the characteristics: 0.867 g/mL of density; 5.72 cSt of viscosity; 1.449 of refractive index; 1.46 g KOH/g of acid number; and 0.023% of water content. Identification of GC-MS obtained the synthesized methyl esters, which include: 46.10% of methyl hexadecanoic, 41.68% of methyl 9-octadecanoic, 6.42% of methyl octadecanoic, and 5.80% of methyl eicosanoic.