Conventional mechanical ventilation (CMV) has been recommended as the first-line mode of respiratory support for neonates born with a congenital diaphragmatic hernia (CDH). However, older studies suggested that protective high-frequency oscillatory ventilation (HFOV) with low-mean airway pressure (MAP) may limit lung injury. We aimed to compare low-MAP HFOV with CMV in neonates with CDH in terms of patient outcomes. This retrospective cohort study was conducted in two French neonatal intensive care units: center 1 mainly used CMV, and center 2 mainly used HFOV with a low MAP. All term neonates with CDH born between 2010 and 2018 in these two centers were included. The primary outcome was the duration of oxygen therapy. Secondary outcomes were survival and duration of mechanical ventilation. A total of 170 patients (105 in center 1, 65 in center 2) were included. In center 2, 96% of patients were ventilated with HFOV versus 19% in center 1. After adjustment for perinatal data, there was no significant difference regarding duration of oxygen therapy (SHR 0.83, 95% CI [0.55–1.23], p = 0.35) or survival (HR 1.73, 95% CI [0.64–4.64], p = 0.28). Center 2 patients required longer mechanical ventilation and sedation.