Senior administration officials did not divulge the contents of the records being shared by the National Archives on Thursday.
Conspiracy theories have swirled since President Kennedy was fatally shot in Dallas, Texas, 54 years ago. A 1992 law passed by Congress required all records related to the assassination - around five million pages - to be publicly disclosed in full within 25 years. The deadline was Thursday. Now, more than 90 percent of the files were already in the public domain.
Allegations of a government cover-up are unlikely to be assuaged by reports that the CIA, FBI, Department of State and other agencies lobbied at the last minute to keep certain documents under wraps.
In a memo directing heads of executive departments to release the files, Trump said the American public deserves to be "fully informed about all aspects of this pivotal event".
"Therefore, I am ordering today that the veil finally be lifted," the president wrote.
Some redacted documents are undergoing a further six-month review, but it is possible those records could stay secret after the deadline on 26 April next year.
The president, according to White House officials, was reluctant to agree to agency requests to hold the remaining documents.
"I have no choice - today - but to accept those redactions rather than allow potentially irreversible harm to our Nation's security," Trump added in his memo.
The records are being released on the National Archives website.