A 39-year-old female with systemic lupus erythematosus (SLE) with a neurogenic bladder is described. She developed voiding disturbance with paraplegia and sensory disturbance on her inferior limb. Clinical findings suggested elevated activities of SLE with transverse myelitis. Although her symptoms were improved after one course of methylprednisolone pulse therapy, clean intermittent catheterization was required for urinary incontinence and residual urine. One year later, bilateral hydronephrosis and vesical diverticulitis developed, and thus augmentation ileocystoplasty was performed. After three months of the operation, hydronephrosis and urinary incontinence resolved with frequent clean intermittent catheterization. We should not overlook lower urinary tract symptoms in patients with SLE. We advocate performing a surgical procedure in cases in which conservative treatments are not effective.