Introduction—the upper airway panendoscopy, performed under general anesthesia, is mandatory for the diagnosis of cervicofacial cancer. It is a challenging procedure because the anesthesiologist and the surgeon have to share the airway space together. There is no consensus about the ventilation strategy to adopt. Transtracheal high frequency jet ventilation (HFJV) is the traditional method in our institution. However, the COVID-19 pandemic forced us to change our practices because HFJV is a high risk for viral dissemination. Tracheal intubation and mechanical ventilation were recommended for all patients. Our retrospective study compares the two ventilation strategies for panendoscopy: high frequency jet ventilation (HFJV) and mechanical ventilation with orotracheal intubation (MVOI). Methods—we reviewed all panendoscopies performed before the pandemic in January and February 2020 (HFJV) and during the pandemic in April and May 2020 (MVOI). Minor patients, patients with a tracheotomy before or after, were excluded. We performed a multivariate analysis adjusted on unbalanced parameters between the two groups to compare the risk of desaturation. Results—we included 182 patients: 81 patients in the HFJV group and 80 in the MVOI group. After adjustments based on BMI, tumor localization, history of cervicofacial cancer surgery, and use of muscle relaxants, the patients from the HFJV group showed significantly less desaturation than the intubation group (9.9% vs. 17.5%, ORa= 0.18,p= 0.047). Conclusion—HFJV limited the incidence of desaturation during upper airway panendoscopies in comparison to oral intubation.