Acting on specific information, the police and army launched a joint operation in Medhikona village under Dhupdhara police station in the district, police said.
The militant in a bid to escape opened fire following which the security forces retaliated killing the ultra, they said.
The police recovered a hand grenade and a 9 mm pistol from the slain militant.
A joint team of the police and army had killed two GNLA militants in an encounter in Borjhora village under Lakhipur police station of the same district on the night of October six.
GNLA is an insurgent outfit based in Meghalaya's Garo Hills region adjoining Goalpara district.