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Background: Studies of cortical atrophy in migraine and tension-type headache (TTH) have reported inconsistent results. Some studies have reported decreased cortical thickness or volume, while others have reported thickening in the somatosensory and visual cortices in migraine patients. The same controversy is true with respect to episodic and chronic headaches. This study evaluated and compared cortical atrophy in migraine and TTH as well as in episodic and chronic headache. Methods: The study included 43 (37 female) migraine and 15 (12 female) TTH patients. Demographic, clinical, and brain magnetic resonance imaging (MRI) data were evaluated. 1.5 Tesla MRI brain coronal T2 sequences were reviewed by two neurologists, and atrophy was graded according to a visual rating scale (VRS). Two neurologists jointly evaluated and scored cortical thickness on a Likert scale of 0 to 3 or 4 at the following sites bilaterally: olfactory sulcus, anterior cingulate sulcus, circular insular sulcus, anterior temporal and medial temporal lobes, and posterior cingulate and parieto-occipital sulci. The scores at all sites were then summed into a total atrophy score (TAS) for each subject. Results: There was no significant difference between the migraine and TTH groups regarding demographics, clinical findings, and atrophy scores in any particular region or with respect to the TAS. When we divided our study subjects into episodic and chronic headache groups, there was no significant difference between these groups in terms of demographic and clinical findings or individual and total atrophy scores. Conclusions: These results are in line with previous studies that have reported no differences between migraine and TTH in terms of cortical atrophy.