Methanol is a commonly used acyl acceptor for lipase-driven biodiesel production, but a high concentration of methanol is detrimental for lipase activity. To overcome this drawback, a simple fed-batch process was developed by optimization of the methanol feeding strategy and reaction conditions. For the feeding strategy, an equal volume of pure methanol was fed twice with specified time intervals into a reactor initially containing a 1:1 molar ratio of soybean oil to methanol in order to adjust the net molar ratio of the oil to methanol to 1:3. In contrast with the batch reaction, a higher agitation speed in the fed-batch process elevated the conversion yield of soybean oil to biodiesel. An agitation speed of 600 rpm and a reaction temperature of $70^{circ}C$ were chosen as the optimal environmental conditions. Residual lipase activities for the fed-batch operation at $40{sim}70^{circ}C$ and 600 rpm were $7.1{pm}1.4$ times higher than that of the batch method at $40^{circ}C$ with the same agitation speed, indicating that methanol feeding can prevent significant deactivation of lipase. Finally, two times feeding methanol at 2 and 6 hr resulted in a biodiesel productivity of 10.7%/h and 94.9% final conversion yield under the optimal conditions.