<p>Podocyte infolding glomerulopathy is a rare glomerular lesion characterized by microtubular structures and microspheres in the glomerular basement membrane. While most reported cases are associated with autoimmune diseases such as systemic lupus erythematosus, pediatric cases are rarely reported. The patient was a 14-year-old Japanese girl with a 1-year history of proteinuria detected during a school urinary screening program. Five months prior to admission to our department, she was hospitalized at a regional hospital for acute abdominal pain. Although her symptoms resolved spontaneously, a renal biopsy was performed due to the presence of proteinuria, leukopenia and antinuclear antibody positivity. However, the diagnoses of systemic lupus erythematosus was not established at that time owing to negative IgG, IgA, IgM, C3 and C1q on immunofluorescence, negative anti-dsDNA and anti-Smith antibody as well as normal serum C3 and C4 levels. On admission to our department, she was diagnosed with systemic lupus erythematosus and lupus enteritis based on the presence of malar rash, fever, leukopenia, and proteinuria supported by the characteristic findings on abdominal enhanced computed tomography. Reassessment of the initial renal pathology revealed microtubular structures and microspheres within the glomerular basement membrane on electron microscopy, consistent with podocyte infolding glomerulopathy. Induction therapy with methylprednisolone pulse therapy improved her systemic symptoms and proteinuria promptly. This is the first report of podocyte infolding glomerulopathy in a pediatric patient with systemic lupus erythematosus. Clinicians should be aware of this unique glomerular lesion in pediatric-onset systemic lupus erythematosus.</p>