Brett Dieter, 52, of Barbersville, Virginia, arrived at the upstate New York airport on Friday to pilot a flight to New York City's LaGuardia International Airport for Piedmont Airlines, a passenger airline that subcontracts under US Airways.
While at a security checkpoint, a scan of Dieter's bag revealed a .357 magnum revolver loaded with five rounds. It was not immediately clear if the pistol was in his carry-on luggage.
Federal prosecutors in Buffalo allege he began traveling with the weapon when he reported for work on May 16 on a flight from Charlottesville, Virginia, to LaGuardia, but skipped a security screening of his baggage.
"The defendant did not submit this bag to X-ray screening at the Charlottesville airport," the federal indictment states.
Deiter, and the gun, traveled on "several other flights" over a two-day period, prosecutors allege.
He is charged with unlawfully possessing a concealed firearm, a charge punishable by 10 years in jail and a $250,000 fine.
US Attorney William Hochul, whose office in Buffalo is handling the case, said Dieter shouldn't have been allowed to carry the gun, although sometimes, exceptions are made for law enforcement officials.
"In this day and age, we simply can't afford to have anyone ignore these important regulations," he said in a statement issued following the arrest.
Dieter is due in court next week to answer the charge.
U.S. airline pilots who receive special training may carry guns in the cockpit but are not allowed to have them elsewhere in the plane or in airport terminals. The program began some 10 years ago following the September 11, 2001 aircraft hijacking attacks.