The attackers – believed to be from the Boko Haram group – destroyed the entire village of Mainok, about 50km (30 miles) west of the city of Maiduguri.
The incident took place late on Saturday, hours after two bomb blasts killed at least 50 people in Maiduguri.
Boko Haram has been conducting a four-year violent campaign to demand Islamic rule in northern Nigeria.
The morning after the latest attack, bodies were lying in front of the mosque waiting to be buried and buildings in Mainok were still on fire, the BBC’s Will Ross reports from Lagos.
An eyewitness described how the attack unfolded: “They started shooting everywhere, they started burning all the houses in the village.
“I don’t think that there is any house that is standing in the village and they have killed at least 39 people in the village.”
CNN reports as of half an hour ago that dozens of people have been killed in three attacks. The first casualties were in a village bombed by a military plane trying to bomb Boko Haram camps on Friday night.
Dozens of attackers in military uniforms stormed the village of Mainok on Saturday evening, riding four-wheelers and motorcycles, as residents were preparing for evening prayers.
“They came in around 7 p.m. and opened fire indiscriminately with RPGs (rocket propelled grenades), explosives and AK-47 rifles,” said Mainok resident Yahaya Umar. “They killed 39 people who were buried this morning and destroyed the whole town.”
The attack on Mainok came soon after two explosions in Maiduguri, 50 kilometers away.
“We were just lamenting the twin blasts in Maiduguri at the soccer viewing center when the Boko Haram gunmen arrived and started firing volleys of RPGs and guns,” Abdullahi Gana said. The Mainok resident added that some of the victims were burnt in their homes while others were shot as they tried to flee.
More corpses for Allah.