We describe a woman with systemic lupus erythematosus presenting with nephropathy after the complete resection of a thymoma and the adjacent thymic gland. The woman showed no symptoms of autoimmune disorders or nephropathy at operation. One year later, however, she noticed arthralgia, and laboratory examination showed mild proteinuria, leukopenia, a high level of serum antinuclear antibody (1:1280), anti-dsDNA antibody, and a low level of complement. Renal biopsy showed focal necrotizing glomerular lesions, suggestive of lupus involvement. The pathogenesis of lupus erythematosus in our case is briefly discussed in relation to preceding thymoma and its resection.