In recent years, the production and consumption of fossil jet fuel have increased as a consequence of a rise in the number of passengers and goods transported by air. Despite the low demand caused by the coronavirus 2019 pandemic, an increase in the services offered by the sector is expected again. In an economic context still dependent on scarce oil, this represents a problem. There is also a problem arising from the fuel's environmental impact throughout its life cycle. Given this, a promising solution is the use of biojet fuel as renewable aviation fuel. In a circular economy framework, the use of lignocellulosic biomass in the form of sugar‐rich crop residues allows the production of alcohols necessary to obtain biojet fuel. The tools provided by process intensification also make it possible to design a sustainable process with low environmental impact and capable of achieving energy savings. The goal of this work was to design an intensified process to produce biojet fuel from Mexican lignocellulosic biomass, with alcohols as intermediates. The process was modeled following a sequence of pretreatment/hydrolysis/fermentation/purification for the biomass‐ethanol process, and dehydration/oligomerization/hydrogenation/distillation for ethanol‐biojet process under the concept of distributed configuration. To obtain a cleaner, greener, and cheaper process, the purification zone of ethanol was intensified by employing a vapor side stream distillation column and a dividing wall column. Once designed, the entire process was optimized by employing the stochastic method of differential evolution with a tabu list to minimize the total annual cost and with the Eco‐indicator‐99 to evaluate the sustainability of the process. The results show that savings of 5.56% and a reduction of 1.72% in Eco‐indicator‐99 were achieved with a vapor side stream column in comparison with conventional distillation. On the other hand, with a dividing wall column, savings of 5.02% and reductions of 2.92% in Eco‐indicator‐99 were achieved. This process is capable of meeting a demand greater than 266 million liters of biojet fuel per year. However, the calculated sale price indicates that this biojet fuel still does not compete with conventional jet fuel produced in Mexico. © 2022 Society of Chemical Industry and John Wiley & Sons, Ltd.