In the thoracolumbar region, between 7% and 30% of spinal fusion failures are at risk for pseudarthrosis. From a biomechanical perspective, the nonconformity of the intervertebral graft to the endplate surface could contribute to pseudarthrosis, given suboptimal stress distributions. The objective of this study was to quantify the effect of endplate-graft conformation on endplate stress distribution, maximum Von Mises stress development, and stability. The study design used an experimentally validated finite element (FE) model of the L4–L5 functional spinal unit to simulate two types of interbody grafts (cortical bone and polycaprolactone (PCL)-hydroxyapatite (HA) graft), with and without endplate-conformed surfaces. Two case studies were completed. In Case Study I, the endplate-conformed grafts and nonconformed grafts were compared under without posterior instrumentation condition, while in Case Study II, the endplate-conformed and nonconformed grafts were compared with posterior instrumentation. In both case studies, the results suggested that the increased endplate-graft conformity reduced the maximum stress on the endplate, created uniform stress distribution on endplate surfaces, and reduced the range of motion of L4–L5 segments by increasing the contact surface area between the graft and the endplate. The stress distributions in the endplate suggest that the load sharing is greater with the endplate-conformed PCL-HA graft, which might reduce the graft subsidence possibility.