The Swedish teenage environment activist will interview the veteran broadcaster during a special climate edition of the programme.
The 16-year-old Nobel peace prize nominee said it would be the first time the pair had spoken.
“We’ll be reporting about the scale of the ongoing climate crisis and I’ll be talking to David Attenborough for the first time,” she said in an announcement about the interview.
Sir David has previously celebrated Greta’s “passion” for climate change activism.
The broadcaster backed her appearance at the UN Climate Summit in October, telling The Huffington Post: ”Greta Thunberg is there because of her passion, her insight and her concern about the future.
“She’s a political person, she’s not a broadcasting person.”
Greta, who began holding Friday protesters outside her country’s parliament in August 2018, has inspired millions of young people to call for faster action against climate change.
She was named Time magazine’s Person of the Year for 2019.
The Today programme has announced several guest editors between 26 and 31 December, including artist Grayson Perry, former Telegraph editor Charles Moore, rapper George the Poet and Supreme Court president Baroness Hale.