Army Secretary John McHugh used a torch to transfer the flame, The Washington Post reported. He was accompanied by Col. Michelle Stewart, the cemetery's acting chief of staff, and escorted by a military honor guard.
The flame was moved to a nearby temporary holder several months ago while repairs were carried out at the memorial.
Kennedy was buried at Arlington in Virginia on Nov. 25, 1963, three days after he was assassinated in Dallas. His wife, Jacqueline, lit the eternal flame.
The president's body and the flame were transferred to a permanent memorial site at Arlington three years later.