Other celebrities including Tom Hanks, Robert De Niro and Michael Jordan were also among the 21 recipients of the country’s highest civilian honor.
President Obama said it was easy to forget the risk Ellen DeGeneres took to come out as gay in 1997.
During the award ceremony at the White House, he said Ellen DeGeneres’ bravery helped “push our country in the direction of justice”.
“It’s easy to forget now, when we’ve come so far… just how much courage was required for Ellen to come out on the most public of stages almost 20 years ago,” President Obama said.
“What an incredible burden that was to bear – to risk your career like that – people don’t do that very often. And then, to have the hopes of millions on your shoulders.”
The Presidential Medal of Freedom, which recognizes contributions to United States culture, security and international interests, is the highest honor a civilian can receive, alongside the Congressional Gold Medal, a similar accolade awarded by the US Congress.
“These are folks who have helped make me who I am,” Barack Obama said.
“Everybody on this stage has touched me in a very powerful, personal way, in ways that they probably couldn’t imagine.”
Honorees from the entertainment world included Tom Hanks, Robert De Niro, Robert Redford and Cicely Tyson, as well as musicians Bruce Springsteen and Diana Ross.
From the sporting world, former basketball superstars Kareem Abdul-Jabbar and Michael Jordan were awarded the medal, alongside sports broadcaster Vin Scully.
Bill and Melinda Gates were awarded for their philanthropic work through their charitable foundation.
Despite Barack Obama’s words on the contribution Ellen DeGeneres made to the country, she almost missed the ceremony after security refused to let her in to the White House.
Ellen DeGeneres tweeted alongside a photo of herself sitting on a nearby park bench: “They haven’t let me in to the White House yet because I forgot my ID.”
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