Biodiesel fuel is one of the most attractive alternatives to the traditional diesel fuel derived from a petroleum refinery. Development of a reliable model for the biodiesel production process requires maximizing economics and enhancing safety in the commercial operation of biodiesel plants. We propose a model which represents effectively the non-catalytic biodiesel production reaction. In the modeling of the reaction, we employ a nonlinear programming scheme to estimate reaction kinetic parameters which minimize a specified objective function. The behavior of the methanol during the reaction is investigated both experimentally and numerically. Imperfect mixing in the liquid phase at the initial reaction stage causes a little discrepancy between the experimental data and results of simulations. Overall, the proposed model represents the biodiesel production reaction effectively.