Clear cell odontogenic carcinoma (CCOC) is an uncommon condition that has been considered malignant since 2005. The clinical presentation usually involves an asymptomatic swelling, which typically affects the anterior mandible in middle-aged women; it has neither clinical nor radiological defining features. Immunohistochemical analysis usually aids diagnosis, as clear cells are also associated with other clear cell carcinomas and benign tumors. Radical surgery is the gold standard of treatment and usually needs microsurgical reconstruction with bone transference for restoration of facial anatomy and adequate function. We present the case of a young woman with CCOC whose tumor removal and reconstructive surgery were planned virtually and assisted by intraoperative navigation. The novelty of the reconstructive procedure was the replacement of the fibula cutting guides for intraoperative navigation of the osteotomies. We present a brief review of CCOC and the benefits of using computer-assisted surgery (CAS) in high-complexity cases like this one.