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A man in his 50s was referred to our hospital after recurrent severe urinary tract infection. He had undergone anoplasty for anorectal malformation during early infancy. He noticed urinary leakage from the anus for a long time. Under diagnosis of congenital rectourethral fistula, we performed fistula closure. The fistula was transsected via transperineal incision and each stump was closed. A gracilis muscle flap approximately 30 cm long was harvested from the left thigh, brought into the deepest part between the separated rectum and urethra through a subcutaneous tunnel and fixed there. The urinary leakage from the anus disappeared, and the infection resolved. Application of gracilis muscle flap for congenital diseases is rare, but was useful in the present case.