The 25-year-old was one of two Queens men arrested early Friday in connection with the investigation of Najibullah Zazi, a Colorado airport driver who pleaded not guilty last year to supporting terrorism.
The indictment made public by prosecutors on Saturday provided scant details on the accusations against Medunjanin, who was born in Bosnia but is a U.S. citizen.
It said the charges were related to a trip he made to Pakistan in August of 2008. Prosecutors have said that Zazi, Medunjanin and a third man, Zarein Ahmedzay, traveled there together that summer.
All three attended high school together and lived for years in the same Queens neighborhood.
Zazi has been under arrest since September, charged with getting explosives training from al-Qaida and later hatching a foiled scheme to attack targets in New York with homemade bombs. The new indictment did not directly tie Medunjanin to the New York plot - what Attorney General Eric Holder has called one of the most serious terrorism cases since the Sept. 11, 2001, terror attacks.
Outside court, defense attorney Robert C. Gottlieb told reporters that his client's not guilty plea was "emphatic." He accused authorities of holding and interrogating Medunjanin for two days without letting him see his family or a lawyer.
"The questioning was illegal," Gottlieb said. Prosecutors declined to comment.
Ahmedzay pleaded not guilty Friday to charges that he lied to the FBI during the probe about places he visited during the 2008 trip. He was taken into custody early Friday morning while working a late-night shift driving a cab in Manhattan.
Ahmedzay, 24, and Medunjanin were first publicly linked to the investigation in September, when the FBI raided their homes shortly before Zazi's arrest.
FBI agents had Medunjanin under surveillance, but apparently did not intend to arrest him when they went to his Queens apartment Thursday afternoon to seize his passport. Once that happened, authorities say he became upset and took off in his car.
A law enforcement official confirmed reports that Medunjanin then phoned 911 and ranted in Arabic, "We love death more than you love life," before purposely ramming his car into another vehicle and fleeing on foot.
The official was not authorized to discuss the arrest and spoke to The Associated Press on condition of anonymity.
After being captured and treated for minor injuries, federal investigators took him into custody. There were no signs of injury Saturday when he appeared in court wearing a black hooded winter jacket and entered his plea in a firm voice.
Gottlieb suggested that the car incident had been overblown, saying, "Let's see what the evidence is."
Medunjanin was ordered held without bail until a hearing Thursday.