Purpose To investigate choroidal vascular changes using an image binarization tool in patients with clinically unilateral pseudoexfoliation syndrome (XFS). Methods This cross-sectional study included 150 eyes of 100 patients. The eyes were divided into three groups: (1) 50 affected eyes of patients with clinically unilateral XFS; (2) 50 unaffected fellow eyes; and (3) 50 healthy control eyes. Enhanced depth imaging optical coherence tomography scans of the macula and peripapillary regions were acquired. Images were binarized using ImageJ software (National Institutes of Health, Bethesda, MD, USA). The choroidal vascularity index (CVI) was defined as proportion of the luminal area to the total circumscribed choroidal area. Results Horizontal and vertical scans revealed that the macular CVI values of the affected eyes (60.08 +/- 2.06 and 62.21 +/- 2.10, respectively) were lower compared with control eyes (67.31 +/- 2.24;p = 0.001 and 68.11 +/- 2.36;p < 0.001, respectively). Conversely, no significant difference in the macular CVI was found between unaffected fellow and control eyes (p = 0.094 andp = 0.120, respectively). The mean peripapillary CVI values of the temporal (58.73 +/- 3.15), superior (59.84 +/- 3.09), and inferior (56.94 +/- 2.47) sectors were significantly lower in affected eyes compared to control eyes (63.21 +/- 3.00, 62.07 +/- 3.05, and 60.78 +/- 2.88, respectively;p < 0.05 for all). In addition, the unaffected fellow eyes had significantly lower CVI values in the temporal (61.42 +/- 3.07) and inferior (57.61 +/- 2.56) peripapillary sectors compared with the control eyes (p = 0.007 andp = 0.005, respectively). Conclusions These findings suggest that XFS is associated with decreased macular and peripapillary choroidal vascularity. Furthermore, the unaffected eyes of patients with unilateral XFS may show vascularity changes in the peripapillary choroid.