He died at his home on Monday, his son Jamie confirmed to The New York Times.
With the Kennedys, Stoughton documented the nation's famous first family in their shining public moments and their intimate private ones and, in a signal image of the 20th century, Lyndon B. Johnson's swearing-in as president aboard Air Force One on Nov. 22, 1963.
Stoughton's picture is the only photographic record of the Johnson administration's abrupt, official beginning after President John F. Kennedy was assassinated in Dallas.
Assigned by Army public relations to photograph Kennedy's inauguration, he so impressed the new president that he soon became the first full-time White House photographer. He stayed on with the Johnson administration until 1965.
Cecil William Stoughton was born on Jan. 18, 1920, in Oskaloosa, Iowa. He studied voice at what was then William Penn College in Oskaloosa but left to join the Army before the United States entered World War II. He was assigned to a photography training program and a career was born.
He is survived by his second wife, the former Faith Hambrook; their children, Jamie, Bill and Sharon Houghton; a son from his first marriage, Stephen, six grandchildren; and a great-grandchild.