Objective The aim of this study was to conduct a detailed ophthalmological examination in children with systemic lupus erythematosus (jSLE), including choroidal thickness (ChT), choroidal vascularity index (CVI) and peripapillary retinal nerve fiber layer (RNFL). Methods The study included all jSLE patients (n = 21) diagnosed according to the Systemic Lupus International Collaborating Clinics classification criteria between January 2017 and April 2017, and an age- and gender-matched control group (n = 21). The Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) was used to assess disease activity. After routine eye examinations, ChT at five points (750 mu and 1500 mu from the center of the fovea both in the temporal and nasal quadrants and under the fovea), total subfoveal choroidal area (TCA), luminal area (LA), stromal area (SA), CVI and RNFL thickness at the optic disc were evaluated. Results One patient had active ocular involvement in the form of episcleritis. Another patient had corticosteroid-induced cataract. The median age of the patients was 16 years (6-19 years). ChT at five points, TCA, LA and SA were found to be higher in patients with jSLE, whereas RNFL thickness and CVI were similar to those of the healthy control individuals. No correlation was determined between optical coherence tomography findings, SLEDAI and the immunological parameters (antinuclear antibodies, anti-double-stranded DNA, complements 3 and 4, extracted nuclear antigen antibody, antiphospholipid antibody). Intraretinal and subretinal fluid was not present in any of the patients. Conclusion The choroid was thicker in patients with jSLE than in the control group. The study results suggest that jSLE may affect the choroid. Ophthalmological evaluation is important in SLE patients, even in the absence of relevant complaints.