The medal is the nation's highest honor for a civilian. The individuals were chosen based on their contributions to the security or national interests of the U.S., world peace, and for cultural or other significant accomplishments.
"These outstanding men and women represent an incredible diversity of backgrounds," Obama said in a statement.
"Their tremendous accomplishments span fields from science to sports, from fine arts to foreign affairs," he said. "Yet they share one overarching trait: Each has been an agent of change. Each saw an imperfect world and set about improving it, often overcoming great obstacles along the way."
U.S. Rep. Jackie Speier, D-San Mateo, praised Obama for selecting Milk, a pioneer, she said, who "dedicated and sacrificed his life so that others might live in a world free of discrimination."
"My hope now is that, along with honoring the man, we also honor his work by making the United States of America a land of true equality and freedom," Speier said. "Harvey Milk will receive his real and rightful honor when our nation sheds the last vestiges of our intolerant past."
Other recipients are Nancy Goodman Brinker, Pedro Jose Greer, Jr., Stephen Hawking, Jack Kemp, Sen. Edward Kennedy, Billie Jean King, the Rev. Joseph Lowery, Joe Medicine Crow, Sandra Day O'Connor, Sidney Poitier, Chita Rivera, Mary Robinson, Janet Davison Rowley, Desmond Tutu, and Muhammad Yunus.
Obama will present the awards at a ceremony on Aug. 12.