Primary squamous cell carcinoma of the rectum is extremely rare. Squamous cell carcinoma of the anorectum is a known entity evaluation and treatment protocols have been well defined. The occurrence of squamous cell carcinoma of rectosigmoid in concurrence with squamous cell carcinoma of the anal canal is extremely rare and the first case to be reported in the literature. A 48-year-old male patient presented with difficulty in passing stools. The clinical examination, colonoscopy, and the histopathology revealed synchronous proctosigmoid and the anorectal neoplasm. A case like this will pose a diagnostic challenges; squamous cell carcinoma of the rectum is not defined in the medical literature; synchronous squamous cell carcinoma will pose both diagnostic dilemmas and treatment challenges like whether to conserve the sphincter or not. Because squamous cell carcinoma of the anorectum can be treated by chemoradiotherapy, even this case is initially thought of treating by neoadjuvant chemoradiotherapy followed by low anterior resection followed by adjuvant treatment. Since there was no medical literature to support this treatment, ultimately multidisciplinary tumor board decision was made for abdominoperineal resection. Patient was treated with abdominoperineal resection and adjuvant chemoradiation. The diagnostic dilemmas and the management issues have been discussed.