"Yesterday, on my orders, United States forces captured Mustafa al-Imam in Libya," Trump said in a statement, which came as the White House was rocked by the indictment of three campaign aides.
Trump said "al-Imam will face justice in the United States for his alleged role in the September 11, 2012 attacks in Benghazi."
Attorney General Jeff Sessions confirmed that the suspect "will face justice in federal court for his role in the attack."
The attack killed US ambassador Chris Stevens as well as three other American personnel and became emblematic of conservative opposition to then secretary of state Hillary Clinton.
Several congressional investigations were launched, along with a State Department security review, into both the handling of the attack and how it was described in the media.
Clinton was never convincingly tagged with wrong-doing or negligence, but the issue haunted her failed 2016 presidential campaign and may have contributed to Trump's victory.