The president of the west African country said that 80 jihadists were killed in subsequent clashes with security forces.
The violence, which erupted in the town of Arbinda in Sahel region near the country's border with Mali, lasted for several hours, according to a military statement.
Seven members of the security forces who responded also were killed.
Jihadist incursions are frequent in the area but the number killed in the latest attack is unprecedented.
"The heroic action of our soldiers has made it possible to neutralise 80 terrorists," President Roch Marc Christian Kabore said. "This barbaric attack resulted in the death of 35 civilians, most of them women."
It was not immediately clear where the women were at the time of the attack and why so many died.
There was no immediate claim of responsibility for the attack. A number of Islamic extremist groups are known to operate in Burkina Faso, though they generally do not usually come forward when civilian casualties are high.
Frequent attacks in the country's north and east already have displaced more than a half million people, according to the United Nations.
At least 37 civilians were killed in the east last month when suspected jihadists ambushed a convoy carrying employees of Canadian mining company Semafo in eastern Burkina Faso.
In the past Burkina Faso had largely been spared the sort of Islamist attacks that had afflicted neighbouring countries.
In a 2013 French-led military intervention was needed in Mali to dislodge jihadists from power in several major towns.
However an attack in 2016 in Ouagadougou, the capital of Burkina Faso, which left 30 dead, saw the start of a Jihadi terror campaign, which the government has so far been unable to contain.
