Ahmed Abu Khattala was captured by US forces in Benghazi on June 18.
He denied a raft of terrorism-related charges. He says he was in Benghazi during the attack on the US consulate but that he did not take part.
The US ambassador to Libya, Chris Stevens, and three other people were killed in the September 2012 attack.
Ahemed Abu Khattala was charged with providing material support and resources to terrorists including himself; killing a person on a federal facility; and damaging property of the US by fire and explosives resulting in death.
The next hearing was set for July 8.
American media reported that Ahmed Abu Khattala was brought to court in Washington from a US Navy warship where he had been held since being captured two weeks ago.
The US has described Ahmed Abu Khattala as “key figure” in the attack on the consulate.
President Barack Obama praised the raid which led to his capture earlier this month.
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