Soldiers set up a base in the area of the three borders between Mali, Burkina Faso and Niger. File photo/AFP

A militant attack in northern Burkina Faso on Tuesday killed 35 civilians, almost all of them women, the president said, one of the deadliest assaults in nearly five years of militant violence in the West African country.

Seven soldiers and 80 militants were also killed in the double attack on a military base and Arbinda town in Soum province, the army said.

Burkina Faso, bordering Mali and Niger, has seen regular militant attacks which have left hundreds dead since the start of 2015 when militant violence began to spread across the Sahel region.

"A large group of terrorists simultaneously attacked the military base and the civilian population in Arbinda," the army chief of staff said in a statement.

"This barbaric attack resulted in the deaths of 35 civilian victims, most of them women," President Roch Marc Christian Kabore added on Twitter, praising the "bravery and commitment" of the defence and security forces.

Communications minister and government spokesman Remis Dandjinou later said 31 of the civilian victims were women, adding around twenty soldiers were injured.

The president has declared 48-hours of national mourning.

The morning raid was carried out dozens of militants on motorbikes and lasted several hours before armed forces backed by the air force drove the militants back, the army said.

No group immediately claimed responsibility for the attack, but militant violence in Burkina Faso has been blamed on militants linked to both Al Qaeda and Daesh groups.