Desmoid tumors are rare, benign, but locally aggressive fibromatoses that pose significant therapeutic challenges, particularly when located in the head and neck region. This report details the case of an extensive cervical desmoid tumor dependent on the levator scapulae muscle and involving the vertebral artery managed through surgical resection and intraoperative navigation. A 45-year-old male presented with a slowly growing cervical mass. Imaging revealed an 83x68x40 mm mass in the right lateral paravertebral space, dependent on the levator scapulae muscle and involving the vertebral artery. Biopsy confirmed a low-grade fusocellular myofibroblastic neoplasm consistent with a desmoid tumor. Given the poor prognosis associated with the symptomatic mass, surgical resection was performed using Brainlab intraoperative navigation (Brainlab, Munich, Germany). The procedure was successful, with preservation of vital structures and no evidence of recurrence postoperatively. Desmoid tumors in the head and neck region, though rare, require precise diagnostic and therapeutic approaches due to their aggressive nature and proximity to critical anatomical structures. The use of intraoperative navigation, in this case, facilitated accurate tumor resection, minimizing damage to surrounding tissues. Pathological analysis revealed a CTNNB1 gene mutation, specifically the S45P variant, which is associated with an increased risk of recurrence. This case highlights the importance of a multidisciplinary approach, incorporating advanced surgical techniques and genetic analysis, in the management of complex desmoid tumors. Intraoperative navigation proved invaluable in achieving successful surgical outcomes, underscoring its potential utility in similar cases. Continued follow-up is essential, given the potential for recurrence associated with desmoid tumors.