The station opened as Minatomachi Station (湊町駅) on March 1, 1899. It was renamed JR Namba on September 4, 1994, in collaboration with the opening of Kansai International Airport. New underground facilities opened on March 22, 1996, and replaced the former above-ground station.
The tracks from the Kansai Main Line are expected to be extended north from this station by 2031 with the completion of the Naniwasuji Line. The new line is to be routed through central Osaka and will terminate at new underground platforms at Osaka Station.