While this movie carries the same name as the book "Thirteen Days" by former Attorney General Robert F. Kennedy, it is in fact based on a different book, "The Kennedy Tapes: Inside the White House During the Cuban Missile Crisis" by Ernest R. May and Philip D. Zelikow. In contrast to The Missiles of October (1974), which was based on Kennedy's book, this film contains some newly declassified information not available to the earlier production, but takes greater dramatic license, particularly in its choice of Kenneth P. O'Donnell as protagonist.
The destroyer Joseph P. Kennedy was loaned to the movie company by the Battleship Massachusetts Foundation in Fall River, Massachusetts. In addition to being named for a Kennedy brother killed in WWII it was actually part of the Cuban Blockade. The ship was towed to Narragansett Bay for filming. The ship is normally on display in Fall River.
(February 1, 2001) First film to be screened at the White House by President George W. Bush and Laura Bush. In attendance at the historic screening were members of the Kennedy family, members of Congress and personal friends of the President and First Lady.
In the early briefing scene where Arthur Lundahl, director of the CIA's National Photographic Interpretation Center, shows a map of the missiles' range, the town of Oxford, Miss., is one of the targets. All other targets were major US cities. This was not an error. It's not clear whether the joke started with the Kennedys or the CIA, but in any case President John F. Kennedy was still smarting from the previous month's riots in Oxford, which put him at cross-purposes with a recalcitrant segregationist Gov. Ross Barnett of Mississippi and some US army generals -- notably Gen. Edwin Walker -- whose hesitation to dispatch troops to northern Mississippi bordered on insubordination. Kennedy was said to have quipped "Can they hit Oxford?" when told about the missiles.
Although the F-8 aircraft used in the movie are real aircraft once used by the Philippine Air Force, they were, in fact, nonfunctional at that time. During the filming of the movie, the planes were actually being towed.
After John F. Kennedy leaks the Walter Lippmann column to the press, and the representative from Russia is on the television expressing his concern, Kennedy (Bruce Greenwood) struggles with his tie and clearly mouths an expletive that gets overdubbed as a sound of frustration to maintain the PG-13 rating. In his next line, he mouths that the representative is "fucking killing us," and again his line is overdubbed to remove the curse.
The aircraft shown carrying the President to Connecticut is an actual VC-137 (Boeing 707) Presidential aircraft used by President John F. Kennedy. The 707 shown wasn't in service until a month after the Cuban crisis, though. At the time another 707 with a different color scheme was used.