Background: Endometriosis of the cervix is a rare, non-cancerous disease that can look or behave like cancerous cervical tissue, causing challenges regarding diagnosis and management. Discrimination between benign and malignant lesions can be difficult when utilizing cytological, colposcopic, and histopathological data if the findings do not agree with each other. Case Presentation: We report the case of an asymptomatic 45-year-old woman who was initially diagnosed with FIGO stage IA1 microinvasive cervical carcinoma based on cytological, colposcopic, and conization findings. Further evaluation yielded persistent uncertainty in diagnostic imaging and, in addition, a concern for invasive cervical disease. Therefore, the patient underwent a total hysterectomy with bilateral salpingo-oophorectomy, and the result of the postoperative evaluation was cervical endometriosis without evidence of invasive malignancy. This example demonstrates the diagnostic challenges associated with rare benign cervical lesions, which may resemble cervical carcinoma, and emphasizes the high-risk for overtreatment due to the vagueness of these types of cases. Conclusions: When there is a discrepancy among clinical findings, cytology, and histopathology in suspicious cervical lesions, cervical endometriosis must be considered in the differential diagnosis. To increase accuracy in diagnosis and minimize the possibility of unnecessary radical treatment, careful histopathologic reevaluation and multidisciplinary assessment are necessary.