The putsch was announced after the presidential guard stormed a cabinet meeting, detaining the Interim President and Prime Minister.
A close ally of ex-President Blaise Compaore has been named the new leader.
World leaders and the African Union (AU) have condemned the takeover.
At least three people have been killed by the presidential guard, RSP, amid protests in the capital, Ouagadougou.
Report says that an unknown number of protesters have also been detained.