Apnoeic oxygenation is not only important for patients who cannot be intubated/ventilated, but also can be routinely employed when planning to secure the airway.We aimed to compare safe apnoea times between patients receiving modified nasopharyngeal oxygen therapy and those receiving high-flow nasal oxygen therapy (HFNO) following the induction of general anaesthesia.This was a single-centre, randomized controlled clinical study. Eighty-four female patients undergoing elective laparoscopic gynaecological surgery under general anaesthesia were randomly assigned to the high-flow nasal oxygen therapy group (Group HFNO) or the modified nasopharyngeal oxygen therapy group (Group Naso). A Kaplan–Meier survival curve was used to describe the apnoeic oxygenation time.The safe apnoea time of the patients in the Group Naso was higher than that of the patients in the Group HFNO (20 (19.3 to 20.0) vs. 16.5 (12.9 to 20) minutes, P < 0.05). The incidence of SpO2 < 95% in the Group Naso was lower than that in the Group HFNO; hazard ratio 0.3 (95% confidence interval 0.2 to 0.6, P < 0.0001). Modified nasopharyngeal oxygen therapy which uses far less oxygen than HFNO is a convenient and effective method of apnoeic oxygenation in normal female patients.Trial registration: https://www.chictr.org.cn, ChiCTR2000039433; date of registration: 28/10/2020.