It’s Brain-gate!

John F. Kennedy’s noodle didn’t get buried with him on Nov. 25, 1963, at Arlington National Cemetery — and his own brother might have been behind the theft, a new book claims.

“Not all the evidence from the assassination is at the National Archives. One unique, macabre item from the collection is missing — President Kennedy’s brain,” writes James Swanson in “End of Days: The Assassination of John F. Kennedy,” which comes out Nov. 12, just a few weeks before the 50th anniversary of JFK’s death.

During JFK’s autopsy at Bethesda Naval Hospital, the brain was placed in a stainless-steel container with a screw-top lid.

“For a time, the steel container was stored in a file cabinet in the office of the Secret Service,” writes Swanson.

The brain was later placed in a footlocker with other medical evidence and taken to the National Archives, where it was “placed in a secure room designated for the use of JFK’s devoted former secretary, Evelyn Lincoln, while she organized his presidential papers.”

“In October 1966, it was discovered that the brain, the tissue slides and other autopsy materials were missing — and they have never been seen since,” Swanson told The Post.

An investigation was ordered by then-Attorney General Ramsey Clark, but the probe failed to recover the missing brain — which remains unaccounted for today, Swanson said.

But it did “uncover compelling evidence suggesting that former Attorney General Robert Kennedy, aided by his assistant Angie Novello, had stolen the locker,” according to Swanson.

Conspiracy theorists have posited that the brain was stolen to conceal evidence that the president was shot from the front — perhaps from the grassy knoll — instead of the official version of events, that the gunfire came from the rear, from the Texas School Book Depository.

Swanson rejects that the brain vanished as part as a nefarious plot to hide the facts of the assassination.

“My conclusion is that Robert Kennedy did take his brother’s brain — not to conceal evidence of a conspiracy but perhaps to conceal evidence of the true extent of President Kennedy’s illnesses, or perhaps to conceal evidence of the number of medications that President Kennedy was taking,” he said.