During the 1940s, the American Medical Association and the
National Committee on Physical Fitness had a joint committee encouraging physical fitness.
The President's Council on Youth Fitness was founded on July 16, 1956, to encourage American children.
In 1963, President Kennedy changed the council's name to President's Council on Physical Fitness to reflect its role to serve all Americans.
In 1966, President Lyndon B. Johnson created the Presidential Physical Fitness Award, the name of which was later changed to President's Challenge Youth Physical Fitness Awards Program. In 1968, the council's name was changed to President's Council on Physical Fitness and Sports to emphasize the importance of sports in life.
In 1972, the Presidential Sports Award Program was created.
In 1983, the United States Congress declared May as National Physical Fitness and Sports Month.
In 1996, the Surgeon General's Report on Physical Activity and Health was released. In 1997, the Council released its report on Physical Activity and Sport in the Lives of Boys.
In June 2010, President Barack Obama renamed the agency the President's Council on Fitness, Sports and Nutrition, with a new emphasis on nutrition as an element of fitness. First Lady Michelle Obama announced the new commission's goal "to end the epidemic of childhood obesity in a generation" and also announced that the president had named, as the new co-chairs of the council, New Orleans Saints quarterback Drew Brees and former Olympic gymnast Dominique Dawes.
On January 11, 2012, operators of the website for participants of the Challenge and Active Lifestyle programs learned that the site had been hacked, resulting in the release of personal information of the participants. The President's Challenge site displayed a notice that it was down for "Site Maintenance – We're taking a little breather." On January 20, 2012, the site was modified to explain the hacking. On January 27, 2012, The President's Challenge sent out emails to its participants saying that the website was functional as of January 24, 2012, and asked participants to reset their user passwords.