In 2010, the rock band sued its longtime label for digitally selling tracks of "unbundled" music from their original albums.
Pink Floyd won early on in the court battle, but the case dragged on as EMI made an unsuccessful appeal.
EMI said Tuesday that "all legal disputes between the band and the company have been settled as a result of this new deal," which will see EMI continue to market and distribute Pink Floyd's catalog.
Pink Floyd signed with EMI in 1967. The record label also has The Beatles, Coldplay and Lily Allen on its books.
The Associated Press contributed to this report.