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Abstract Background Primary squamous cell carcinoma of the endometrium is an extremely rare tumor with poorly understood pathogenesis. Case presentation We report a case of a 28-year-old Togolese woman who had consulted for vaginal bleeding and pelvic pain. Ultrasound showed thickening of the lining of the endometrium, and biopsy curettage was done. Anatomopathological examination was noteworthy for a proliferation of squamous cells often connected by union bridges arranged in tumor lobules with dyskeratotic maturation. Immunohistochemistry showed epithelial membrane antigen positivity, anti-pancytokeratin 1 markers of tumor cells positivity, chromogranin A negativity, actin negativity, S100 negativity, estrogen receptor negativity, and progesterone receptor negativity. In situ hybridization had objectified human papillomavirus genotypes 16/18. The diagnosis of primary squamous cell carcinoma of the endometrium associated with human papilloma virus was retained. A hysterectomy was performed, and the tumor was classified pT1N0M0. Conclusion The pathogenesis of this endometrial cancer is complex, and its association with human papillomavirus does not explain its genesis.