"I am optimistic that we will see an increase in the numbers of passengers traveling between our countries," said U.S. Ambassador John Roos, after signing the treaty in Tokyo.
Airlines including Japan Airlines Corp. and United Continental Holdings (UAL) now plan to collaborate on schedules and sales.
Japan is seeking to boost tourism and is opening up new flight slots at its airports.
"It opens up great opportunities for airlines on both sides of the Pacific," said Geoff Tudor, principal analyst for Japan Aviation Management Research. "It enhances each carrier's network and in turn, that helps customers who can make journeys through one carrier that perhaps they couldn't have made before."