In this manuscript, we describe a case of lupus nephritis with diffuse podocytic infolding in the glomerular basement membrane (GBM). A 23-year-old woman presenting with proteinuria, leukopenia, a high value of antinuclear antibody, and positive for anti-dsDNA and anti-Sm antibodies was diagnosed with systemic lupus erythematosus. A renal biopsy was performed which showed diffuse change in the GBM and focal segmental mesangial hypercellularity under light microscopy. The GBM showed diffuse mild thickening and diffuse irregular stippling (bubble-like appearance) on staining with periodic acid-silver methenamine. However, spike formation was only occasionally seen. An immunofluorescence study was conducted which revealed fine granular deposition of IgG (2+) along the glomerular capillary walls; however, granular deposits of C1q (1+) and C3 (1+) were primarily detected in the mesangial areas. Diffuse irregular GBM thickening with dispersed distribution of microspheres and microtubules was observed using electron microscopy. In addition, these structures were chiefly detected on the epithelial side of the GBM. Since these structures seemed to connect to podocytes, we believed that the formation of these microspheres and microtubules is caused by the infolding of podocytes. This case shows a unique pathological finding, and may belong to a new glomerular disease entity characterized by podocytic infolding. After a renal biopsy, the patient received oral prednisolone 0.8 mg/kg day initially, and her complete remission status continued for 5 years.