MIRAGE syndrome is a rare multisystem disorder caused by gain-on-function SAMD9 variants. Kidney biopsies in some MIRAGE syndrome patients have shown glomerular sclerosis or interstitial nephritis. A boy with genetically confirmed MIRAGE syndrome, who showed microhematuria and nephrotic range proteinuria, underwent kidney biopsy at 18 months, revealing diffuse mesangial proliferation and partial segmental lobular accentuation associated with mesangial cell proliferation with neither crescentic lesions nor sclerotic glomeruli. Immunofluorescence staining showed diffuse granular deposition of IgG along the glomerular basement membrane and dominant deposition of IgG in the mesangial matrix. Electron microscopy revealed diffuse subepithelial electron-dense deposits. Treatment with prednisolone for membranous nephropathy-like findings was initiated but the proteinuria persisted. At 21 months of age, the patient died of multi-organ failure as a result of severe gastrointestinal infection and necrotizing enterocolitis. This is the first case with histologically membranous nephropathy-like findings and marked mesangial proliferation in a child with MIRAGE syndrome with nephrotic syndrome.