Background In 2003, a perinatal helicopter air ambulance service was introduced for remote areas of Wakayama and Mie prefectures, Japan. However, its long-term impact on perinatal medicine has not yet been analyzed. Methods A retrospective observational study was conducted on helicopter air ambulance cases recorded between January 2003 and December 2016 at Wakayama Medical University Hospital (WMUH). Results During that period, 61 pregnant mothers were transferred by helicopter air ambulance to WMUH. Between 2003 and 2009, the mean period from transfer to birth was 0.6 weeks, whereas between 2008 and 2016, this increased to 1.6 weeks, and the survival rate of infants who were born after transfer did not differ significantly (84.2% [32/38] and 82.1% [23/28]). Seventy-three neonates were transferred. The number transferred between 2003 and 2009 was 46, whereas this decreased to 27 between 2010 and 2016. The neonatal mortality rate in south Wakayama plus south Mie gradually decreased. The reasons for the longer period from transfer to birth, and the decrease in the rate of very low birth weight infants after transfer may be developments in the management of threatened premature labor, and the earlier transfer of such cases by regional obstetricians. The reasons for the decline in neonatal transfer cases may have included the development of fetal diagnostic techniques and improved efficiency of neonatal ground-transport in the South Wakayama region. Conclusions The helicopter air ambulance is an important form of medical transportation in the south Kii peninsula. This article is protected by copyright. All rights reserved.