There is global pressure to make advanced biofuels profitable. For cellulosic ethanol, three aspects remain as bottlenecks: collection of feedstocks, pretreatment methods, and enzyme production. In this paper, the first aspect is investigated, by addressing the main challenges for the logistics of agricultural residues. A logistic supply chain of corn stover collection and utilization for cellulosic ethanol production in Mexico is proposed, and a cost structure is designed for its estimation. By applying a value chain methodology, seven links and a set of three minimum selling prices (MSPs) of agricultural residues were determined. Furthermore, the harvest index (HI), crop residue index (CRI), nutrient substitution by extraction of agricultural residues, and harvest costs of corn stover were also calculated for a case study. The main results were a HI of 0.45, a CRI of 1.21, and nutrient substitution potential of 7 kg N, 2.2 kg P ₂O ₅, and 12.2 kg K ₂O per ton of corn stover. The set of the three estimated MSPs for corn stover was: $28.49 USD/ton (for delivery to the biorefinery’s gate), $31.15 USD/ton (for delivery and storage), and $48.14 USD/ton (for delivery, storage, and nutrient replenishment). Given the impact of the feedstock cost on the profitability of cellulosic ethanol, knowing details of the logistical information and its costs is critical to advancing the field of biofuels in Mexico. We also found that only 20% of farmers currently sell their residues; however, 65% of farmers would be willing to do so, a significant percentage for cellulosic ethanol production.