Fractures of the equine metacarpophalangeal (MCP) joint are among the most common and fatal injuries experienced by racehorses. These bone injuries are a direct result of repetitive, high intensity loading of the skeleton during racing and training and there is consensus that they represent a mechanical fatigue phenomenon. Existing work has found the fatigue life of bone to be strongly determined by bone microarchitecture and the resulting stressed volume (i.e., the volume of bone stressed above yield). The purpose of this study was to quantify the influence of bone microarchitecture on the mechanical fatigue behaviour of equine subchondral bone from the MCP joint. Forty-eight subchondral bone samples were prepared from the third metacarpal (MC3) and proximal phalanx (P1) and subsequently imaged using high resolution micro-computed tomography (μCT) to quantify microarchitectural features of interest, including bone volume fraction, tissue mineral density, pore size, pore spacing, and pore number. Samples were cyclically loaded in compression to a stress of 70 MPa, and fatigue life was defined as the number of cycles until failure. Finite element models were created from the μCT images and used to quantify the stressed volume. Based on the expected log point-wise predictive density (ELPD), stressed volume was a strong predictor of fatigue life in both the MC3 and P1. Normalized stress (i.e., initial nominal strain) was also a strong predictor of fatigue life in samples from the MC3, but not for samples from the P1. This disparity can be attributed to differences in microstructure homogeneity. A regional analysis indicated fatigue life was more strongly associated with bone volume fraction in the superficial (r² = 0.32, p < 0.001) and middle (r² = 0.70, p < 0.001) regions of the subchondral bone, indicating that the cortical plate plays a more prominent role in the fatigue resistance of subchondral bone. By improving our understanding of the variance in fatigue life measurements, this research helps begin to clarify the underlying mechanisms of the mechanical fatigue process and provide a basic understanding of subchondral bone injuries in the equine fetlock joint.