A 60-year-old female presented to our hospital with anal pain. Colonoscopy (CS) revealed a tumor in the anal canal, which was diagnosed as squamous cell carcinoma by biopsy. Computed tomography (CT) showed multiple liver metastases. From these findings, we diagnosed the anal tumor as stage IV squamous cell carcinoma of the anal canal. Although CS and CT indicated disappearance of the primary tumor and liver metastases following chemoradiotherapy, brain metastasis developed during the disease course and was treated with radiotherapy and surgical resection. Administration of S-1 as adjuvant chemotherapy was continued, and the patient has remained alive for approximately six years without recurrence. To the best of our knowledge, this case can be considered as having the longest-term survival in stage IV squamous cell carcinoma of the anal canal.