Abstract: The SEPN1 gene encodes selenoprotein N, and mutations in this gene can cause SEPN1-related myopathy (SEPN1-RM). SEPN1-RM is an extremely rare and complex congenital myopathy with an insidious onset and slow progression, often leading to multi-system involvement. The main clinical manifestations include axial and proximal muscle weakness, early respiratory dysfunction, and spinal deformities. This article reports the diagnosis and treatment conditions for a pediatric patient carrying novel mutation in SEPN1 gene who underwent spinal orthopedic fusion surgery. After detailed multidisciplinary evaluation, adequate preoperative preparation, and meticulous perioperative management, the patient successfully underwent high-risk spinal orthopedic surgery and recovered well. Based on the patient's diagnosis, perioperative management, and follow-up, combined with a review of the latest domestic and international literature, this article systematically discusses the diagnostic and therapeutic characteristics of this rare disease. The aim is to enhance clinicians' understanding of such diseases and to provide evidence-based support and reference for perioperative comprehensive management strategies for rare diseases.