The band will close the Isle of Wight event, which takes place between September 9 and September 12.
The 'Warrior's Dance' collective join a bill that already includes Roxy Music, LCD Soundsystem, The Flaming Lips and Dizzee Rascal.
The Wailers and Wild Beasts have also been announced to appear, while Zane Lowe and La Roux are due to play DJ sets.
"Since raving as a young pup to 'Charly' and 'Out Of Space' through to caning their new record on my radio show, The Prodigy have been a massive part of my record collection," said organiser Rob Da Bank of The Prodigy's inclusion on the lineup.
"As far as polishing off the party on Sunday night, I can't think of a more explosive finale... and it's going to be the last we'll see of them for quite a while on our shores - so get in the queue now!"
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