He follows previous guests such as disgraced politician Neil Hamilton, eco-warrior Swampy, Liberal Democrat leader Charles Kennedy and actress Maureen Lipman.
Sir Elton will be on Paul Merton's team on Friday's edition of the show, while Ian Hislop will be joined by journalist Janet Street-Porter.
The singer's appearance on the show, notorious for its caustic treatment of guests, comes after a difficult few months for him.
Difficult
In October 2000, Sir Elton appeared in court as part of legal action against his former manager Andrew Haydon and accountants PricewaterhouseCoopers (PwC).
The court case lasted 43 days, and included the revelation that he once spent £40m over a 20 month period, including £293,000 on flowers.
In April 2001 the judge found in favour of Mr Haydon and PwC, leaving Sir Elton with an estimated £8m in legal costs.
A week after the ruling, Sir Elton put 20 of his prized classic cars up for auction, saying he did not have enough time to drive them.
He also courted controversy in February 2001 by dueting with controversial rapper Eminem at the Grammy awards in the United States.
Biting wit
The programme has been notoriously hard on its guests at times. Former deputy Labour leader Roy Hattersley was once booked to appear, but failed to attend.
Rather than book a last-minute replacement, Paul Merton's team-mate was a tub of lard.
Similarly, Merton once had former spy David Shayler as his guest. Shayler was unable to re-enter the UK without being arrested, so his seat was replaced by a widescreen television upon which Shayler appeared via live satellite link from France.