Stoughton died Monday evening at his home on Merritt Island, Fla., his son Jamie Stoughton said.
The photo he took of the swearing-in ceremony aboard Air Force One in Dallas, Johnson with his hand raised and a stunned Jacqueline Kennedy looking on, became the most famous in his five years, 1961-65, as White House photographer.
"Cecil Stoughton's photos helped to create the aura that later came to be called Camelot," said Bobbi Baker Burrows, director of photography at Life magazine and coauthor of the National Geographic Society's 2006 publication, "The Kennedy Mystique."
"In the confusion that followed the assassination, his [swearing-in] photograph told the world that there was a new president, and the country that it was safe," Burrows said.
Stoughton was born in Oskaloosa, Iowa, on Jan. 18, 1920. He was an Army captain in 1961 when he was picked by Kennedy's military aide, Maj. Gen. Chester Clifton, to photograph events at the White House. He was the first official White House photographer.
During those years he became close to the Kennedy family.
Accompanying Kennedy to Dallas on Nov. 22, 1963, Stoughton was in the fifth car in the motorcade and heard the shots that fatally wounded the president. He was at Parkland Hospital, where Kennedy died, when he learned he had to photograph the swearing-in before Air Force One left for Washington, D.C.
Stoughton's work is now archived at the John F. Kennedy Presidential Library and Museum in Boston.
Cecil Stoughton later worked as a National Park Service photographer, his son said.
In 1973 he published a book, "The Memories -- JFK, 1961-1963," with Clifton and Time magazine writer Hugh Sidey.