Thompson was released on his own recognizance after his lawyer entered the plea. He's charged with carrying a pistol without a license and carrying an unregistered firearm and unregistered ammunition.
Authorities say Thompson was arrested Monday when he entered the office building with a loaded pistol and two other loaded magazines in a briefcase that he placed on an X-ray machine. He's quoted in court documents as saying the weapon belonged to Webb.
Sen. Jim Webb said Tuesday that the arrest was "enormously unfortunate" and "unintentional."
Webb refused to say flat out that it was his gun but made it clear that he is sometimes armed, CBS News correspondent Bob Fuss reports.
He wouldn't say how his aide ended up carrying the gun into the Capitol, but suggested it was a mix-up involving various bags left behind when he flew out of town.
Webb said that because Thompson was being arraigned Tuesday, he can't specifically discuss the case.
Capitol police have said the weapon was revealed when Thompson went through an X-ray machine Monday at an entrance of the Russell Senate Office Building.
Capitol Police spokeswoman Sgt. Kimberly Schneider said the aide was charged with carrying a pistol without a license and possessing an unregistered firearm and unregistered ammunition.
Webb's office said Monday that Thompson was "a former Marine, a long-term friend and trusted employee of the senator."
A congressional official briefed on the incident said Webb gave the gun to Thompson when the assistant drove him to an airport earlier in the day. Thompson, upon entering the Senate building, forgot he was carrying the weapon.