There is growing interest in the horse for behavioral, neuroanatomic and neuroscientific research due to its large and complex brain, cognitive abilities and long lifespan making it neurologically interesting and a potential large animal model for several neuropsychological diseases. Magnetic resonance imaging is a powerful neuroscientific research tool, that, although can be performed in-vivo with adapted equine facilities, could become a routine ex-vivo tool in equine research. The brain atlas is a fundamental resource for neuroimaging research, being vital for assessment of in-vivo and ex-vivo imaging data. Brain atlases have been created for a multitude animal models however none currently exist for the equine brain. In this study we document the creation of a high-resolution stereotaxic population average brain atlas of the equine. The atlas was generated from nine unfixed equine cadaver brains imaged within 4 hours of euthanasia in a 3-tesla MRI. The atlas was generated using linear and non-linear registration methods and quality assessed using signal and contrast to noise calculations. Tissue probability maps (TMPs) for white matter, grey matter and cerebrospinal fluid, were generated and manually segmented anatomic priors created for multiple subcortical brain structures. The resulting atlas is correlated to gross pathological specimens and is made freely available at as an online resource for researchers. The mean volume metrics for the whole brain, grey matter and white matter for the included subjects were documented and the effect of age and laterality assessed. Alterations in brain volume in relation to age were identified, though these variables were not found to be significantly correlated. All subjects had higher whole brain, grey matter and white matter volumes on the right side, consistent with the well documented right forebrain dominance of horses. This atlas provides an important tool for automated processing in equine and translational neuroimaging research.