A batch process was developed for biodiesel production from high free fatty acid feedstocks. The mixed-integer nonlinear programming (MINLP) problem caused due to applying of hierarchical procedure together with Malone’s algorithm for conceptual design was solved. Meanwhile, the optimum states of major process parameters such as the utilization of process equipments, paralleling, splitting, and merging of unit operations, process cycle time (CT), and combination of batch and continuous units were determined. Based on the present optimization study, the optimum value of process cycle time and the optimum number of the esterification reactors in series were obtained as 3.257 h/batch and 3 stages, respectively. The batch process was found to be suitable for a capacity of less than 260 tons/yr, while the continuous process was suitable for a capacity of greater production rates. The results showed that the production rate had a direct effect on the economic potential of the process and that it should be set at its maximum possible practical value. Also, the break-even point at the optimum state occurred at 130 tons/yr of production rate.