The objective of this study was to evaluate the measurements of choroidal thickness (CT) in patients with non-arteritic anterior ischaemic optic neuropathy (NAION) at the acute and chronic stages. This case-control study compares three groups: Group 1 included 23 eyes of 23 patients with chronic NAION, Group 2 consisted of 24 eyes of 24 patients with acute NAION, and Group 3 included 24 eyes of 24 age-matched control subjects. The average CTs for Group 1, Group 2, and Group 3 were 261.24 ± 50.04, 280.05 ± 74.94, and 254.74 ± 50.11 µm, respectively. For all measurements, no statistical significance was found between the groups (p = 0.319, 0.357, 0.680, and 0.178 for the CTs as average, foveal, superior, and inferior, respectively). Similarly, there was no difference between the CT measurements of the affected and unaffected eyes in Group 1 and Group 2 (p = 0.571, 0.741 for average, respectively). The amount of time after the onset of the disease ranged from 6.0 to 48 months (23.86 ± 16.70 months) in Group 1 and from 1 to 30 days (7.45 ± 8.86 days) in Group 2. There was no correlation between the CTs and follow-up times in Group 1 (p = 0.768 for average) and no association between the CTs and the thicknesses of the retinal nerve fibre layers in Group 2 (p = 0.453 for average). CT is not directly influenced by NAION at either the acute or the chronic stage of the disease. These results may also demonstrate that the changes of CT do not increase the risk of experiencing a NAION attack.