The patient was a 47-year-old man with a 24-year history of anal fistula. A carcinoma associated with anal fistula was diagnosed after a biopsy was performed because the anal fistula was not improving. Computed tomography and magnetic resonance imaging showed that the tumor had invaded the spongy urethra. Therefore, preoperative chemotherapy(S-1 plus radiation at a dose of 60 Gy/body) was performed. Because the size of tumor decreased, we performed abdominoperineal resection with reconstruction using a gracilis musculocutaneous flap, which enabled the spongy urethra to be fully preserved. Histopathologically, no cancer cells were found to exist on the surgical margin. This case suggested that surgical treatment combined with preoperative chemoradiotherapy may be effective for locally advanced carcinoma associated with anal fistula. Furthermore, improvement of the reconstruction technique for both pelvic and perianal skin defects due to extended resection is an important element of curative surgery.