Purpose To quantitatively analyze the microcirculation in the peripapillary sectors in the affected eyes and fellow unaffected eyes of individuals with unilateral Fuchs uveitis syndrome (FUS) using optical coherence tomography angiography (OCTA), and to compare the radial peripapillary capillary vessel density (RPCvd) with normal and age-matched individuals. Methods Eyes were divided into three groups based on the involvement of the FUS: FUS-positive eye of patients (study eye), fellow eye of FUS-positive patients (fellow eye), and the control eye for the control group (control eye). RPCvd (%) and peripapillary retinal nerve fiber layer (RNFL) thickness (µm) at eight equal sectors and two equal hemispheres were automatically calculated in peripapillary region via OCTA. Results This study included 105 eyes of 71 patients: 34 FUS-positive eyes of 34 patients, 34 fellow eyes of FUS-positive patients, and 37 control eyes of 37 patients. RPCvd was significantly lower in study eyes than in fellow and control eyes in the peripapillary region (p = 0.044 and p = 0.005, respectively). There was no significant difference between fellow eyes and control eyes regarding RPCvd in any region (p > 0.05 for all). There were no significant differences between the three groups regarding peripapillary RNFL values (p > 0.05 for all). Conclusion OCTA is a novel technology for imaging of the RPC network in patients with FUS. Lower radial peripapillary capillary vessel density in FUS could induce capillary insufficiency and impairment of ocular blood flow to optic nerve head.