While it has been shown that repetitive mild brain injuries can cause cumulative damage to the brain, changes to the mechanical properties of brain tissue at large deformations were also noted in the literature. The goal of this study was to show that the viscoelastic properties of brain tissue significantly change after traumatic axonal injury (TAI). An impact acceleration model was used to create TAI in the rat brainstem which was quantified with an immunohistochemistry technique at the ponto-medullary junction (PmJ) and pyramidal decussation (PDx). The viscoelastic properties at these two points with and without preconditioning were characterized using an indentation technique combined with finite element analysis and a comparison was made between injured and uninjured specimens, which revealed statistically significant reduction in the instantaneous elastic force at PDx where the brain tissue sustained a significantly higher level of injury. The result of this study can be used to characterize a damage function for the brain tissue undergoing large deformation.