DeGeneres was one of 21 recipients honoured on Tuesday with the Presidential Medal of Freedom, a prestigious award granted to individuals who have contributed to notable change and progress in the US. Celebrities, among them Tom Hanks, Robert De Niro and Michael Jordan, were also among the 21 recipients.
The outgoing President said it was easy to forget the risk DeGeneres took to come out as gay in 1997. He said her bravery helped "push our country in the direction of justice", reports bbc.com.
Obama choked up as he awarded DeGeneres, and even she got emotional while accepting the award.
"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," Obama said during the award ceremony at the White House.
He added: "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."