The 77-year-old, who is having a procedure on his back, was due to present tonight’s (Friday 13 November) telethon, but has been ordered to rest by doctors.
It will mark the first time that Sir Terry has missed presenting the annual charity show since its launch in 1980.
Sir Terry Wogan has presented every 'Children In Need' fundraiser since its launch in 1980
The BBC have now confirmed that Dermot O'Leary will be stepping into Sir Terry's shoes, with Tess Daly, Rochelle Humes, Nick Grimshaw and Fearne Cotton all serving as co-presenters over the course of the evening.
In a statement, Sir Terry said: "So here we are on the 36th edition of Children in Need, every one of which I've been proud to present since it started in 1980, and for the first time I won't be there to cheer you on with word and gesture to another record-breaking year."
He added: "The British public, as always, will dig deep in their pockets and purses to help the country's disadvantaged children, knowing that every penny will go to those who need it most."
Dermot said: "It's a huge honour to be asked to step into Sir Terry's shoes tonight; he is one of my broadcasting heroes and has been a source of support for me down the years.
"I'd like to add my best wishes to Sir Terry for a speedy recovery, and I hope I do him justice and do my small part to make the night a success and make as much money as we can for disadvantaged children across the country."
Dermot O'Leary will be filling in for Sir Terry Wogan
One Direction, actress Dame Helen Mirren, former ‘Doctor Who’ star David Tennant, Sherlock actor Martin Freeman and singer Ellie Goulding will all be appearing on the show.
This year’s fundraiser is also set to feature a special Star Wars sketch with characters C3PO and R2-D2.
Terry won't be joining the Nick, Tess, Fearne and Rochelle on tonight's show
A BBC spokesman said: "We are so sorry that Terry won't be with us tomorrow night as we know how passionate he is about Children in Need.
"But we wish him a very speedy recovery and know he'll be watching from home and enjoying the show."
Last year more than £32.6m was donate, bringing the total raised to help children and young people across the UK since its launch to £790m.
Watch tonight's Children In Need Appeal at 7.30pm on BBC One.