A federal grand jury indicted Ahmed Abu Khatallah during the rare Saturday session on a single charge of conspiracy to provide material support and resources to terrorists for the attacks that killed US ambassador Chris Stevens and three other Americans two years ago.
He was flown to Washington by helicopter shortly after sunrise from a US Navy warship where he had been held and interrogated since his high-profile capture two weeks ago, a law enforcement official told AFP.
The suspect, believed to be 43 and also known as Ahmed Mukatallah, listened to the court proceedings through an interpreter and raised his right hand before public defender Shelli Peterson entered a not guilty plea on his behalf.
Wearing a dark tracksuit, Abu Khatallah had a long, dark gray beard and mustache with curly hair, court sketches showed. He was not handcuffed.
The case's lead prosecutor warned that the Justice Department could bring additional charges against Abu Khatallah during the ongoing investigation about the assault that saw gunmen storm the US mission in Benghazi and set it on fire.
"Right now, the right move was to not show all your cards at once," a senior law enforcement official explained.
A CIA annex was also targeted in the attacks that shocked Washington, quickly growing into a highly charged political issue.
Abu Khatallah is due back in court, located just a mile (1.6 kilometers) from the White House, on Wednesday for a detention hearing, and again on July 8 for a status hearing.
The US State Department has identified Khatallah as a senior leader of Ansar al-Sharia, a Libyan group responsible for a spate of attacks and assassinations.
US commandos captured Khatallah -- who could face the death penalty -- two weeks ago in a covert raid on Libyan soil.
Libya accused Washington of violating its sovereignty, though it had failed to fulfill an outstanding arrest warrant against Abu Khatallah because of the tense security situation in the flashpoint eastern city of Benghazi.
The raid represents a victory for President Barack Obama, who has faced intense criticism over his administration's handling of the Benghazi assault and its aftermath.
Some Republicans have criticized the administration's decision to try Khatallah in civilian court rather than through the Guantanamo Bay special military tribunals.
Republican Senator Kelly Ayotte expressed "serious concerns that conducting a rushed interrogation onboard a ship and then turning Khattalah over to our civilian courts risks losing critical intelligence that could lead us to other terrorists or prevent future attacks."
- Challenges to the case -
The case relies heavily on accounts from Libyan officials and witnesses who have singled out Khatallah as taking part in the assault that day.
FBI investigators were only able to visit the crime scenes to collect evidence several weeks after the assault due to high security concerns.
Nevertheless, the government is "very confident in our ability to bring this case to prosecution and secure a conviction," a senior law enforcement official said.
"The bottom line is you don't commit the resources we committed to go to the other side of the world apprehending an individual, bringing him on a ship for prosecution if you are not very confident in your case."
FBI Director James Comey hailed Abu Khatallah's capture as a "major step forward" in the investigation, but stressed that the agency's work was not yet over.
"This case remains one of our top priorities and we will continue to pursue all others who participated in this brazen attack on our citizens and our country," he said.
The choice of the US District Court in Washington to try Abu Khatallah was unusual, as most terror suspects tried in the United States since the September 11, 2001 attacks have been tried in federal courts in New York and Alexandria, Virginia.
Khatallah had often been seen in public and defiantly spoke with reporters last year at a luxury hotel in Benghazi.
US officials have dismissed suggestions that the suspect was "hiding in plain sight," or that the operation to capture him could have been conducted much sooner.
The Benghazi attack raised questions about security at US diplomatic facilities worldwide and the accuracy of US intelligence on militant threats.
Republicans charged that the White House failed to respond decisively and then tried to hide some facts in the grisly episode.
The Obama administration, in turn, has accused critics of politicizing a tragic event.