Gen Gilbert Diendere is the most senior official to be charged.
President Sankara was murdered by a group of soldiers, but the exact circumstances of his death have remained a mystery.
Mr Sankara, a left-wing radical described as "Africa`s Che Guevara", remains a hero for many Africans.
He was succeeded by Blaise Compaore who stayed in power for 27 years.
Gen Diendere, who went on to be Mr Compaore`s intelligence chief, was seen as a close friend and political ally of Mr Sankara at the time of his death.
During Mr Compaore`s rule the investigation into the murder made little progress.
Who was Thomas Sankara?
-A captain in army of Upper Volta, a former French colony in West Africa
-Instrumental in the coup that ousted Col Saye Zerbo as president in 1982
-Took power from Maj Jean-Baptiste Ouedraogo in an internal power struggle and became president in August 1983
-Adopted radical left-wing policies and sought to reduce government corruption
-Changed the name of the country from Upper Volta to Burkina Faso, which means "the land of upright men"
-Killed in mysterious circumstances by a group of soldiers in October 1987, aged 37
The transitional government, which took over after Mr Compaore was overthrown in 2014, pledged to investigate the murder.
Ten other officers have already been charged in connection with the death of Mr Sankara.
Gen Diendere is already in detention, facing charges in connection with September`s seven-day coup.
Burkina general helped kill ex-leader
07 December 2015
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The leader of September`s short-lived coup in Burkina Faso has been charged with complicity in the 1987 murder of former President Thomas Sankara.
