The 31-year-old Babyshambles frontman will appear at Thames Magistrates' Court on October 18 along with Pete Wolfe, 42, charged with possessing and supplying cocaine and Alan Wass, 29, who is also charged with possession.
All of the charges relate to an incident that took place between January 21 and 25, according to a Metropolitan Police spokesman.
Doherty was one of four people questioned after the death of Robin Whitehead, 27.
She had been working on a documentary about Doherty but was found dead in a flat in Hackney in January.