The jihadists stormed the barracks early Friday in Nassoumbou, a town near the Malian border that is about 260 kilometers from Burkina Faso's capital, Ouagadougou.
The assailants also set fires to the premises, including tents and military vehicles, a security official told The Associated Press on condition of anonymity as he was not authorised to speak to journalists.
There was no immediate claim of responsibility. This West African country has seen a number of assaults since al-Qaida-linked extremists attacked in Ouagadougou in January, killing 30 people.