The source, speaking on condition of anonymity, told AFP that Compaore, who is living in exile in the Ivory Coast, had been charged with an "attack" and "assassination".
Compaore was toppled from power by a popular uprising in October 2014 after ruling Burkina Faso with an iron fist for 27 years.
Sankara, a revolutionary figure who is still a hero to many in west Africa, was killed on October 15, 1987 during the coup that brought his friend and former comrade-in-arms Compaore to power.
Remains believed to be those of Sankara and 12 former aides also killed during the coup were exhumed from a cemetery in the capital Ouagadougou in May.
At least five other people, mostly former soldiers, have been charged in connection with Sankara's killing -- including General Gilbert Diendere, Compaore's former chief of staff, who led a failed coup in September.