Introduction: Squamous cell carcinomas of the rectum are extremely rare and their pathogenesis is still under debate. Their proper diagnosis and treatment may thus be challenging. Case presentation: A 52-year-old Caucasian woman was transferred to our department with a history of pelvic pain. Colonoscopy revealed a small tumorous lesion of the upper rectum and an endoscopic biopsy showed infiltration of the rectal mucosa by a squamous cell carcinoma. Afterward, tumorous lesions were found on imaging in both her ovaries. A laparoscopy with adnexectomy and anal mapping was performed and revealed tumor masses of squamous cell carcinoma in both ovaries. Based on the large size of the ovarian tumors and the concurrence of extensive, partly ciliated, macrocystic epithelium in one of the ovaries, a diagnosis of ovarian squamous cell carcinoma arising from a mature teratoma was rendered. However, human papillomavirus genotyping analyses were positive for human papillomavirus-16 in both the rectal tumor and ovarian tumors leading to a final diagnosis of a human papillomavirus-associated rectal squamous cell carcinoma metastatic to both ovaries. Neoadjuvant chemoradiation therapy of her rectum, total mesorectal excision, and hysterectomy were performed followed by adjuvant chemotherapy. Conclusion: Colorectal squamous cell carcinoma is a rare disease. In cases of colorectal squamous cell carcinoma, metastatic disease at any other location has to be excluded. Human papillomavirus genotyping is essential in this context. Discussion of the treatment strategies should be interdisciplinary and include chemoradiation therapy and radical surgery.