The dog has been bastioned as a unique and novel animal model for use in neuroscientific and neurocognitive research. As a result, there has been an increase in the use of dogs for non-invasive neuroscience studies generating a need for a standard canine brain atlas that provides common spatial referencing and cortical segmentation for advanced neuroimaging data processing and analysis. In this dataset we create and make available a detailed MRI-based cortical atlas for the canine brain. We create a population template from high-resolution 3-dimensional T1-weighted MRI data obtained from 30 neurologically and clinically normal non-brachycephalic dogs and generate tissue probability maps for grey matter, white matter and the ventricular system. We utilized an additional cohort to test the effect of registration on data from dogs with differing cranial conformations and identified that brains with mesaticephalic or dolichocephalic cranial conformation registered to the template to a high level of similarity with a low degree of warping, whereas brains with brachycephalic cranial conformation exhibited high degrees of warping after non-linear registration. In order to create the cortical atlas, we went on to perform myeloarchitectonic-based cortical parcellation to form 234 priors from frontal, sensorimotor, parietal, perisylvian, occipital, cingular and subcortical regions. This atlas will improve tissue segmentation and cortical region delineation and represents a unique and vital tool to facilitate neuroimaging research in this important animal model.