Clear cell odontogenic carcinoma (CCOC) is a rare, aggressive epithelial neoplasm of the jaw first described in 1985 by Hansen and classified as an odontogenic malignant tumor in the 2005 WHO classification. To date, only 117 cases have been reported in the literature written in English. In this paper, we report the atypical presentation of a pericoronal localized tumor in the right mandibular wisdom tooth discovered during a routine radiologic examination. The patient, a 44-year-old healthy female, was referred by her general dental practitioner for examination of temporomandibular dysfunction and recurrent myofascial pain. Anamnesis and clinical examination did not suggest tumoral disease. The osteolytic lesion was removed, and histological examination revealed a clear cell odontogenic tumor (CCOT) of the right posterior lower jaw. Segmental lower jaw resection was performed, and a free iliac crest bone transplant was fixed with mandibular reconstruction plate. No cervical neck dissection was needed. A five-year follow-up examination shows excellent local and systemic recovery and no sign of tumor recurrence. The patient still suffers from bruxism and myofascial related pain, which are treated conservatively with a Michigan splint and physiotherapy. Based on this additional case, we review the literature and discuss the challenging diagnostic aspects, the unusual clinical presentation, and the treatment of CCOC.