Biodiesel has become attractive due to its environmental benefits compared with conventional diesel. Although the enzymatic synthesis of biodiesel requires low thermal energy, low conversions of enzymatic transesterification with ethanol (ethanolysis) of oils to produce biodiesel are reported as a result of deactivation of the enzyme depending on the reaction conditions. The synthesis of biodiesel via enzymatic ethanolysis of sunflower and soybean oils was investigated. Kinetic parameters for the overall reactions were fitted to experimental data available in the literature with the Ping Pong Bi-Bi mechanism including the inhibition effect of the ethanol on the activity of lipase Novozyme 435. The model was applied to a batch reactor and the experimental conversions were successfully reproduced. The modeling of a semibatch reactor with continuous addition of ethanol was also performed and the results showed a reduction of roughly 3 h in the reaction time in comparison with the batch-wise operation.