Background: Fabry disease (FD) is a X-linked recessive lysosomal storage disorder characterized by altered biodegradation of glycosphingolipids. It is a multisystem pathology, also involving ophthalmological systems that show modifications of the vessel wall due to glycosphingolipid deposits. Optical coherence tomography angiography (OCT-A) allows for an objective analysis of retinal microvasculature alterations, evaluating retinal vessel density in macular region. Methods: A total of 54 FD patients (34 females, 20 males, mean age 44.1 ± 15.6 years) and 70 controls (36 females, 34 males, mean age 42.3 ± 15.6 years) were included in this study. We evaluated vessel density in different macular areas (whole image, fovea, and parafovea) of both the superficial capillary plexus (SCP) and of the deep capillary plexus (DCP). Results: In the SCP there was a significantly lower vascular density in patients compared with controls in whole image (49.95 ± 5.17% vs. 51.99 ± 2.52%; p < 0.001), parafovea (52.01 ± 6.69% vs. 54.30 ± 2.61%; p = 0.002), and fovea (22.38 ± 9.01% vs. 29.31 ± 5.84%; p < 0.0001). In the DCP the vessel density was statistically increased in each macular area in patients compared with controls (54.82 ± 8.07% vs. 50.93 ± 5.46%; p = 0.005, 57.76 ± 7.26% vs. 53.59 ± 5.46%; p = 0.0001, and 39.75 ± 8.59% vs. 34.43 ± 8.68%; p < 0.0001 for whole image, parafovea, and fovea, respectively). Conclusion: OCT-A analysis showed that the macular vessel density was significantly reduced in the SCP and increased in the DCP in FD patients compared with controls. These findings, which might be a consequence of the alteration of vascular wall occurring in FD, support the hypothesis that the evaluation of early retinal microvascular network changes could be a useful tool in the clinical evaluation of the disease.