A White House official said later that the release of the files could be held up if national security or law enforcement agencies believe that is necessary.
"The president believes that these documents should be made available in the interests of full transparency unless agencies provide a compelling and clear national security or law enforcement justification otherwise," the official said.
The thousands of Kennedy documents are set for release by the National Archives on Oct. 26, but it has been unclear if President Trump would block their release on the basis of national security concerns.
The president tweeted Saturday morning that he will allow the release.
Historians and other scholars are eager to sift through the more than 3,000 secret documents on the investigation into the 1963 assassination which over the years has spurred numerous conspiracy theories.
Trump himself dabbled in a conspiracy theory surrounding the Kennedy assassination when during the 2016 campaign he cited an unsubstantiated report that Rafael Cruz, the Cuban-American father of rival GOP primary candidate Ted Cruz, had been photographed with Kennedy assassin Lee Harvey Oswald.
The National Enquirer featured a photo of Oswald handing out pro-Fidel Castro pamphlets in New Orleans in 1963 alongside an unidentified man the Enquirer claimed was Rafael Cruz. The story was uncorroborated and Ted and Rafael Cruz both adamantly denied the allegation after Trump pushed the story in a phone interview with Fox News.