The continuing depletion of fossil fuel reserves and the increasing environmental concerns has encouraged engineers and scientists to look for an alternative, clean, and renewable fuel that can reduce the negative environmental impact. Biodiesel has been considered as one of the best candidate of one of these renewable fuels. One of the pathways to biodiesel production is the transesterification reaction of triglycerides from vegetable oils and short‐chain alcohols. A batch reactor is employed for the production of biodiesel. The flexibility of the batch process allows operating the reactor with different feed stocks and product specifications. This condition becomes challenging for the reactor modeling and control since uncertainty in the feed composition turns into time‐dependent uncertainty and requires a batch‐process based stochastic optimal control. In the first part of this work, the optimal control in this reactor involves optimization of the concentration of fatty acid methyl esters, well known as biodiesel, under the control of reactor temperature and the strategy applied to solve this problem is based on the maximum principle. The strategy increased the concentration by 8.46%. As far as the minimum time required to obtain the same base concentration, it reduced the reaction time by 69.5%.