The 17-year-old, who is currently attending Sidwell Friends School in Washington D.C., made the decision after visiting several public and private universities, and opted for Harvard instead of Princeton and Columbia, where her parents attended.
The President's precocious daughter, who has previously completed an internship on the set of HBO's Girls, will graduate from high school in June before celebrating her 18th birthday on the 4 July.
The White House announced Malia's plans on Sunday
Barack recently revealed that he declined to speak at her graduation ceremony for fear of becoming too emotional. He told Ellen DeGeneres: "I'm going to be wearing dark glasses, sobbing. I'm going to cry."
He continued to speak about the close relationship he shares with his daughter, saying: "I'm not ready for her to leave. She's one of my best friends.
"It's going to be hard for me not to have her around all the time, but she's ready to go. She's just a really smart, capable person and she's ready to make her own way."
Michelle has previously spoken to Seventeen magazine about helping her two daughters Malia and Sasha, 14, choose a university. She said: "The one thing I've been telling my daughters is that I don't want them to choose a name. I don't want them to think, 'Oh I should go to these top schools.' We live in a country where there are thousands of amazing universities. So, the question is: What's going to work for you?"
The President admitted he would find Malia leaving difficult, saying: "it's going to be hard for me"
Malia's exciting news came shortly after her dad delivered a brilliant speech at his last ever White House Correspondents' dinner, where the 54-year-old joked about meeting Prince George.
He feigned offence at the little Prince's nightwear, saying: "some foreign leaders, they've been looking ahead, anticipating my departure. Last week, Prince George showed up to our meeting in his bathrobe. That was a slap in the face. A clear breach of protocol."