A 10-year-old boy was admitted with facial edema and proteinuria for two months, occurring nine months after hematopoietic stem cell transplantation. He was clinically diagnosed with nephrotic syndrome and showed no remission after four weeks of standard glucocorticoid therapy, suggesting steroid-resistant disease. Renal biopsy was consistent with membranous nephropathy. Mass spectrometry identified granular co-deposition of IgG and semaphorin 3B (Sema3B) along the glomerular basement membrane, establishing the diagnosis of Sema3B-associated membranous nephropathy. Treatment with glucocorticoids combined with tacrolimus led to a marked reduction in proteinuria, resolution of edema, and clinical stabilization over a three-month follow-up, with no recurrence. This case highlights that Sema3B-associated membranous nephropathy may occur after hematopoietic stem cell transplantation in children and underscores the importance of precise diagnostics in pediatric nephropathies. Future multicenter studies are needed to clarify disease course and genetic susceptibility, develop specific biomarkers and therapies, promote individualized treatment, and improve prognosis.