The US rapper was confirmed as one of the headliners for the Worthy Farm festival last month, and festival organiser Michael Eavis has previously hinted that he may be joined onstage by other American acts.
The hip-hop star has now revealed he will team up with the nu-metal band on June 29, the day after his Glastonbury show, to perform at the UK leg of the Projeckt Revolution tour. The pair recorded a collaboration album in 2004 called Collision Course.
Other acts that are rumoured to be playing with Jay-Z at Glastonbury include Coldplay, Beyoncé and Kanye West.
Glastonbury takes place on June 27-29. This year's other headliners are The Verve and Kings of Leon.
Tickets for Jay-Z and Linkin Park's show at Milton Keynes Bowl go on sale Friday, March 7.