Low-enriched uranium alloyed with 10 wt. % molybdenum (U-10Mo) has been identified as a promising alternative to highly enriched uranium fuel for the United States’ high performance research reactors. The monolithic U-10Mo fuel plate consists of a metallic U-10Mo fuel foil with a 25 µm Zr interlayer and a relatively thick cladding of aluminum alloy 6061. The Zr interlayer is typically applied during the hot co-rolling process, and this process dictates the uniformity of the Zr interlayer. Thickness variation observed in the U-10Mo and Zr interlayer has been attributed to several sources: the initial grain size of the U-10Mo castings, can materials, rolling temperature, inhomogeneous molybdenum content, and porosity in the cast U-10Mo. This thickness variation limits the ability to meet the dimensional specification; thus, a better understanding of the factors causing the nonuniform thickness is needed. In this work, we used a novel, microstructure-based finite element method to model the hot rolling process to address these concerns. Grain microstructures in U-10Mo were tessellated and explicitly considered in the finite element model. Each grain was assigned a random material property to mimic the grain strength variations induced by different grain orientations. Simulations were performed using six steel can thicknesses, four grain sizes, and with or without a Zr interlayer to investigate the influences of those variables on the thickness nonuniformity. The simulation results showed that a thinner steel can and finer U-10Mo grain size reduce thickness variations in both the U-10Mo fuel foil and Zr interlayer. The direct findings from the simulations and analysis can be used to optimize the hot rolling schedule, reduce fabrication defects, and meet the dimensional specifications. The proposed microstructure-based finite element model can be also coupled with experimental microstructure characterization data, images, and models to simulate multi-pass hot rolling.