Condylar stress fracture of the distal end of the third metacarpal/metatarsal (MC3/MT3) bones is a major cause of Thoroughbred racehorse injury and euthanasia worldwide. Functional adaptation to exercise and fatigue damage lead to structural changes in the subchondral bone that include increased modeling (resulting in sclerotic bone tissue) and targeted remodeling repair (resulting in focal resorption spaces in the parasagittal groove). Whether these focal structural changes, as detectable by standing computed tomography (sCT), lead to elevated strain at the common site of condylar stress fracture has not been demonstrated. Therefore, the goal of the present study was to compare full-field three-dimensional (3D) strain on the distopalmar aspect of MC3 bone specimens with and without focal subchondral bone injury (SBI). Thirteen forelimb specimens were collected from racing Thoroughbreds for mechanical testing ex vivo and underwent sCT. Subsequently, full-field displacement and strain at the joint surface were determined using stereo digital image correlation. Strain concentration was observed in the parasagittal groove (PSG) of the loaded condyles, and those with SBI in the PSG showed higher strain rates in this region than control bones. PSG strain rate in condyles with PSG SBI was more sensitive to CT density distribution in comparison with condyles with no sCT-detectable injury. Findings from this study help to interpret structural changes in the subchondral bone due to fatigue damage and to assess risk of incipient stress fracture in a patient-specific manner.