The singer was recently rumoured to be topping the bill alongside U2 and Coldplay at the event at Pilton Farm, Somerset.
Billboard confirms that Beyoncé will perform a 90-minute headline set on June 26, the final day of the festival.
"This really is the biggest festival in the world and I cannot wait to perform there," Beyoncé said in a statement.
"Everyone who attends is really appreciative of music and is in such a good mood that entire weekend. I'm pumped just thinking about that huge audience and soaking up their energy."
The Libertines have been rumoured to play another reunion gig on the Other Stage during the summer festival.