Background/Objectives: The impacts of the coronavirus disease 2019 (COVID-19) pandemic on patients using helicopter emergency medical services (HEMS) regarding tracheal intubation and patient management remain unclear. Thus, we aimed to investigate this matter in Japan. Methods: In this retrospective, observational study, we analyzed 2277 patients who utilized HEMS in Tochigi Prefecture during 2018–2022. We included only patients who required tracheal intubation. We categorized patients from February 2020 to January 2022 in the pandemic group and those from February 2018 to January 2020 in the control group. We compared the interval from arrival at the scene to leaving the scene (on-scene time) and secondary variables between the two groups. Results: A total of 278 eligible patients were divided into the pandemic group (n = 127) and the control group (n = 151). The on-scene time was lower during the pandemic than that before (25.64 ± 9.19 vs. 27.83 ± 8.74 min, p = 0.043). The percentage of patients using midazolam was lower (11.8% vs. 22.5%, p = 0.02) and that of patients using rocuronium bromide was higher (29.1% vs. 6.0%, p < 0.001) during the pandemic. In contrast, the type of intervention other than tracheal intubation and the type of transportation to the hospital did not differ between the groups. Conclusions: The COVID-19 pandemic was associated with changes in the mission time of and the frequency of certain drugs administered by the HEMS. However, the type of intervention and the type of transportation did not differ. Further research is needed on changes in patient prognosis and condition due to the effects of the COVID-19 pandemic.