Patients with traumatic brain injury (TBI) are severely injured patients who require timely, efficient, and specialized care. The effectiveness of helicopter emergency medical services (HEMS) for patients with TBI remains unclear. This study aimed to compare the mortality of patients with TBI transported by HEMS and ground ambulance using propensity score-matching analysis, and to analyze the effects of HEMS in various subpopulations. We conducted a retrospective analysis of the Japan Trauma Data Bank. The study period was from January 2004 to December 2018. The participants were divided into two groups: the helicopter group (patients transported by HEMS) and ground group (patients transported by ground ambulance). The principal outcome was death at hospital discharge. In total, 58,532 patients were eligible for analysis (ground group, n = 54,820 [93.7%]; helicopter group, n = 3712 [6.3%]). Helicopter transport decreased patient mortality at hospital discharge (adjusted odds ratio [OR], 0.83; 95% confidence interval [CI], 0.74–0.92). In propensity score-matched patients, the proportion of deaths at hospital discharge was lower in the helicopter (18.76%) than in the ground (21.21%) group (crude OR, 0.86; 95% CI, 0.77–0.96). The mortality rate in the helicopter group was significantly reduced in many subpopulations, especially in cases of severe TBI with a decreased level of consciousness or higher Injury Severity Score (ISS; Japan Coma Scale score 2 [adjusted OR, 0.60; 95% CI, 0.45–0.80] and ISS ≥50 [adjusted OR, 0.69; 95% CI, 0.48–0.99]). Although the study design was non-randomized, our findings in patients with TBI showed that HEMS conferred a mortality benefit over ground ambulance.