Primary squamotransitional cell carcinoma (STCC) is rare squamous cell tumor variant resembling transitional cell carcinoma (TCC) of the urinary tract. STCC occurs rarely in the vagina and its clinical and pathological correlates are poorly known. We report a unique case of a 66-year-old Italian woman with STCC of the vagina. A biopsy of the tumor was performed. The tumor qualified as a STCC. Following biopsy, the patient underwent radical hysterectomy (Piver's III-type) with bilateral salpingo-oophorectomy, upper colpectomy, appendicectomy, peritoneal cytology, and lymphadenectomy. The patient is now healthy without evidence of recurrence at 30 months after surgery. Pathologically, cytoarchitectural characteristics distinguish this histotype (STCC) from conventional squamous cell carcinoma of the genital tract. The cytokeratin staining pattern (CK7 positive and CK20 negative), the p63 expression and the positivity for p16ink4a and high-risk HPV are the main elements of differential diagnosis. We suggest that STCC of the vagina should be treated by radical surgery, possibly followed by adjuvant therapy based on staging results and should receive a long-term follow-up.