The incident happened when soldiers of Madras Regiment were conducting routine checking of vehicles near Birat Amguri on NH 52, Superintendent of Police Mugdha Jyoti Mahanta said.
A youth who was travelling in a public transport started firing on the soldiers when they stopped the vehicle.
The armymen retaliated and the youth was killed, the SP said.
Later, two pistols were found on the militant's person.