The aim of the study was to investigate whether retinal neurovascular structural impairment in children with partial biotinidase deficiency (BD) could be detected early via optical coherence tomography (OCT) and OCT angiography (OCTA). Eighty patients with partial BD and 80 control cases without any known systemic or ocular diseases were enrolled in this prospective study. Retinal neurovascular structures in the macular and optic disc regions were examined in using OCT and OCTA. Data from subjects with partial BD were compared with data from healthy controls. A statistically significant decrease in the vessel density (VD) was observed in both superior and inferior parts of the superficial capillary plexus (SCP) and the deep capillary plexus (DCP) in the partial BD patient group compared with the control group (p<0.05). A significant decrease in the VD was also observed in the superior and inferior peripapillary SCP-DCP regions of the optic disc area in the patients with partial BD (p<0.05). Both the superficial and deep foveal avascular zone (FAZ) areas were significantly enlarged in the partial BD group with respect to the control group (p=0.026, p=0.021 respectively). In the partial BD patients, the vascular density in the macula and optic disc region is decreased in childhood, when compared to the control group. In patients with partial BD, it would be very useful to detect the early neurovascular changes that may occur during the course of the disease by means of a noninvasive technique such as OCTA.