Background. We report a case of a squamous cell carcinoma of the right tonsillar region with 5 metastatic lymph nodes and a retropharyngeal metastasis, the latter detected in the preoperative MRI scan. Methods and Results. The treatment consisted of excision of the tumor in the oral cavity and the bilateral neck dissection. Despite careful exploration, a retropharyngeal metastasis was not identifiable during this procedure. This failure encouraged us to use navigation‐guided surgery in a second step. The difficulty in using navigation in soft tissue of the neck is the fixation of the neck. Therefore, a thermoplastic head mask, normally indicated in radiation therapy, was used for both the preoperative CT and navigation‐guided surgery. The retropharyngeal metastasis was successfully excised with this method. Conclusion. This is the first reported attempt to use navigation‐guided surgery in the soft tissue of the neck. It reveals new opportunities for navigation in the future. © 2009 Wiley Periodicals, Inc. Head Neck, 2010