About 97 per cent of the records, which total roughly five million pages, previously held by the archives have now been released.
President Joe Biden said in a statement that a “limited” number of documents would remain top secret at the request of unnamed agencies.
The CIA and FBI have both requested documents be retained in the past.
“Temporary continued postponement of public disclosure of such information is necessary to protect against an identifiable harm to the military defence, intelligence operations, law enforcement or the conduct of foreign relations,” Mr Biden said.
Kennedy was shot and killed by Lee Harvey Oswald while riding through Dallas, Texas, on November 22, 1963. He was 46.
Oswald, a Marine sharpshooter, had at one point attempted to defect to the Soviet Union, returned to the US and then tried to acquire a Russian visa in two different countries. His wife Marina was from the bloc and did not speak English.
For decades, conspiracy theories have abounded over the assassination, which has been the focus of books, movies and podcasts. Some propose foreign governments were involved or that Oswald was a double agent.
None have yielded conclusive proof that Oswald collaborated with anyone and neither do the documents dumped earlier today. Oswald took any and all answers to his grave when he was fatally shot by nightclub owner Jack Ruby, only two days after he killed Kennedy.
Though there were rumours that Ruby killed Oswald to silence him, the nightclub owner said that he did it to save Kennedy's widow from having to relive the nightmare in a trial.
And a newly released document confirms that the CIA found “no indication that Ruby and Lee Harvey Oswald ever knew each other, were associated or might have been connected in any manner”.
The sea of documents includes details about Oswald's visits to Mexico. He entered the country, supposedly by car, at Nuevo Laredo on September 26, 1963, claiming he was a photographer living in New Orleans and bound for Mexico City.
While there, Oswald made several calls to the Soviet embassy, asking in broken English for a visa so he could go to Odessa.
On September 28, he visited the Cuban embassy and Sylvia Duran, a Mexican employee at the Cuban embassy, telephoned the Soviet embassy about his problem.
The release of the documents is in compliance with an October 26, 1992, act of Congress which required that the assassination records held in the National Archives be released in full and unredacted 25 years later.
Agencies contributed to this report