General Gilbert Diendere is expected to face trial before a military tribunal.
Interim President, Michel Kafando, was reinstated two weeks ago after intervention from the Army and West African leaders.
Reports say the presidential guards’ unit that carried out the coup will be disbanded.
General Diendere has been formally charged with 11 crimes including threatening state security, murder, collusion with foreign forces, voluntary assault and wilful destruction of properties.
Former Foreign Minister, Djibril Bassole, who was also arrested in connection with the coup, has also been charged. Mr Bassole has always denied any involvement.
Last week, General Diendere was reported to have surrendered to the authorities in the capital Ouagadougou.
Some of his forces had refused an order to disarm, forcing the Army to attack their base in the city.
The elite Presidential Security Regiment (RSP) is loyal to Compaore, the country’s long-time ruler who was ousted in a popular uprising last year.
Unhappy about being integrated into the regular Army, members of the unit stormed the cabinet’s room on September 16, seizing Mr Kafando, the Prime Minister and others.