The Hokkaido Shinkansen from Tokyo reaches Shin-Hakodate-Hokuto Station in about 4 hours on the fastest Hayabusa services. Shin-Hakodate-Hokuto is about 17 kilometres from central Hakodate, connected by the Hakodate Liner local train (around 17 minutes). This shinkansen link opened in 2016, replacing the slower conventional route through the Seikan Tunnel and bringing Tokyo to easy day-trip distance for the first time — though most visitors still overnight given the distance.
From Sapporo, the conventional JR Hakodate Line takes about 3.5 hours by the fastest limited express (Super Hokuto). A bus from Sapporo takes a similar amount of time but is cheaper. Hakodate Airport has domestic flights from Tokyo (Haneda) and other Japanese cities; the airport is about 9 kilometres from central Hakodate, accessible by bus in about 20 minutes.
A small ferry still runs across the Tsugaru Strait to Aomori for travellers arriving from Honshu without using the shinkansen, though it is infrequently used by tourists given the rail option.