A CIA officer, who was among those accompanying the special forces soldiers, was wounded by the small-arms fire but is expected to survive, officials said.
The casualties were a reminder that U.S. forces in Afghanistan still face grave dangers despite the defeat of the Taliban regime and intensive attacks on the al-Qaida terrorist network.
Some Pentagon officials say the hazards might be even greater now because U.S. soldiers are trying to root out the final few enemy holdouts, who can more easily conceal themselves.
The dead soldier was identified as Sgt. 1st Class Nathan Ross Chapman, 31, of San Antonio, Texas. He was based at Fort Lewis, Washington, with the 1st Special Forces Group.
Army Gen. Tommy R. Franks, commander of the military operation in Afghanistan, said the soldier was part of a team working with Afghan tribes around Gardeyz-Khowst, where some members of the al-Qaida network fled after the U.S. bombardment of the mountainous Tora Bora area to the north.
The Army special forces, also known as Green Berets, have in some cases been working with CIA officers and Afghan fighters to gather intelligence.
"There was an exchange of small-arms fire," Franks said at a news conference in Tampa, Fla., where the U.S. Central Command is based.
"This American serviceman was doing his job. He was out for the purpose of working with and coordinating with tribal leaders in that area."
"Much very dangerous work remains to be done," Franks said, noting that soldiers and Afghan fighters will continue to hunt down the remaining pockets of al-Qaida terrorists and Taliban fighters.
"I am thankful every day that we have not lost more people than we have lost in this fight.
"But I will tell you, in each case when we have lost someone, I think it touches our command and touches all of us very deeply."
The killing of the soldier comes after the deaths of three other Green Berets, who were hit by friendly fire Dec. 5 after they called in a U.S. airstrike and the bomb fell too close to their position outside the southern city of Kandahar.
In addition, Johnny Micheal Spann, a CIA officer, was killed in November during a prison uprising outside the northern city of Mazar-e Sharif.
Just after the meeting ended, the soldiers and the Afghan fighters came under small-arms fire.
The soldier died of his wounds as he was being evacuated by helicopter to a medical facility outside Afghanistan, Quigley said.