As more countries witness depopulation, the expansion of High-Speed Rail (HSR) to reach shrinking cities in peripheral regions is renewing the debate on the effects of this infrastructure. This is the case in Japan, a country that continues to extend its highly developed HSR network hoping to curb regional decline. This paper investigates whether HSR had a positive effect on the shrinking trajectories of connected medium and small-sized cities in peripheral regions by examining the impact of extending the Shinkansen network on five municipalities in the prefectures of Iwate and Aomori, northern Japan. Although depopulation decelerated in some of the case studies, the findings highlight that HSR did not reverse shrinkage and benefits are mainly found in increased accessibility, albeit unevenly distributed. This suggests that, rather than uniformly uplifting socio-economic outlooks, the Shinkansen contributed to reshaping the trajectories of the connected cities and reproduced core–periphery dynamics at the regional level.