Mycotic abdominal aortic aneurysms (MAAAs) are rare but life-threatening, and no standard therapy has yet been established. Effective surgery with intensive antimicrobial therapy is crucial; however, this can be fatal in immunocompromised patients. Only a few reports of MAAA with concomitant autoimmune disease exist; therefore, we were concerned about our lack of experience and knowledge about appropriate treatment. We report a 69-year-old male with an MAAA secondary to septic shock after spinal fusion surgery. He had also been on long-term oral immunosuppressants for systemic lupus erythematosus (SLE). After preoperative cephazolin, we performed debridement of infected tissue, graft replacement with a rifampicin-bonded prosthesis, and omentopexy. On the 52nd post-operative day, he was transferred back to the previous attending hospital under oral antibiotics and prednisolone. MAAA in patients with SLE should be treated with in situ replacement using an antimicrobial prosthetic or biological graft with thorough debridement and omentopexy, followed by antimicrobials and immunosuppressants, as needed.