The reports of chemoradiotherapy for anal squamous cell carcinoma with Crohn's disease are few. Severe toxicity related to radiotherapy is concerned in patients with inflammatory bowel disease. We report a case of chemoradiotherapy for locally advanced fistula-related perianal squamous cell carcinoma in a patient with long-standing Crohn's disease which was controlled by a maintenance therapy. The patient completed standard chemoradiotherapy using intensity-modulated radiotherapy without severe toxicity, and achieved complete remission. Standard chemoradiotherapy using intensity-modulated radiotherapy may be feasible and effective treatment for this population when Crohn's disease is controlled.