The short D4Z4 repeat on chromosome 4q35 is a confirmatory genetic cause of facioscapulohumeral muscular dystrophy (FSHD), which presents with no renal complications. We herein report a five-year-old girl previously diagnosed with Coat's-like retinopathy, deafness, and mental retardation, who was found to have early-onset, severe FSHD. Despite the absence of muscle weakness, a Southern blot analysis showed a short D4Z4 repeat on chromosome 4q35. She presented with steroid-resistant nephrotic syndrome, and her renal histopathological findings were severe glomerular endothelial injury, which is a new complication associated with this genetic abnormality. Screening of renal complications may be necessary for FSHD patients. This patient requires close follow-up for her muscle symptoms.