Waste cooking oil (WCO) is an abundant and inexpensive feedstock for biodiesel production, but conventional homogeneous acid or base catalysts are prone to saponification and are difficult to separate from the reaction product. Enzymatic catalysis using lipase provides a milder and more selective alternative. This study developed a lipase biocatalyst extracted from oil palm (Elaeis guineensis) mesocarp, purified by ammonium sulfate fractionation, and immobilized on activated natural zeolite, for the enzymatic esterification of free fatty acids derived from WCO. Crude lipase activity increased from 3.75 U/mL to 74.08 U/mL after stepwise (NH4)2SO4 precipitation at 60–75% saturation. WCO was first hydrolyzed to free fatty acids (FFA content 2.68% after hydrolysis) and then esterified with methanol at 40 °C for 8 h using free extract, zeolite-immobilized, and commercial lipase at catalyst loadings of 1.2, 1.8, and 2.4% (w/w). Immobilized enzymes produced higher average yields (91.89% for palm lipase and 91.66% for commercial lipase) than free enzymes (79.34% and 87.24%, respectively), and the resulting biodiesel density (0.887–0.898 g/cm3) satisfied SNI 7182:2015. However, viscosity (20.9–22.7 mm2/s) and the GC-MS-confirmed fatty acid methyl ester (FAME) content (9.39% for the free enzyme and 2.76% for the immobilized enzyme) remained far below the SNI requirement, indicating that esterification was incomplete and that further process optimization is required.