Ishigaki has its own airport (New Ishigaki Airport) with direct flights from Tokyo, Osaka, Nagoya, and Naha. The flight from Naha takes about an hour. There are no longer regular ferry services from Okinawa's main island — flying is the only practical way in from outside the Yaeyama chain.
From Ishigaki, ferries run frequently to the surrounding islands of Taketomi (10 minutes), Iriomote (35–45 minutes), and Kohama (25 minutes), all departing from the ferry terminal in Ishigaki town.