Cellulosic biorefineries have attracted interest due to the growing energy security and environmental concerns related to fossil fuel-based energy and chemicals. Using pelleted biomass as a biorefinery feedstock can reduce their processing inputs while improving biomass handling and transportation. However, it is still questionable whether energy and emission savings from feedstock transportation and processing can justify pelletization. A life cycle assessment approach was used to compare energy consumption and greenhouse gas (GHG) emissions from pelleted and non-pelleted corn stover as a biorefinery feedstock. Operations considered were pelleting, transportation, and soaking in aqueous ammonia (SAA) pretreatment. Despite greater GHG emissions (up to 25 times higher than the transportation) generated from the pelleting process, the model showed a significant opportunity to offset and even reduce overall GHG emissions considering the pretreatment process benefits. Our process energy analysis showed that SAA pretreatment of pelleted biomass required significantly lower energy inputs (56%) due to the lower-severity pretreatment’s effectiveness. Higher pretreatment solid loadings are allowed when pelleted biomass is used and this reduces the process chemicals and water requirements by 56% and 49%, respectively. This study demonstrated that the SAA pretreatment of pelleted biomass might be a feasible option as the cellulosic biorefinery feedstock.