The Libertines rocker was formally handed the charge of having the Class A drug on his person when answering bail at a London police station.
Doherty was arrested in March in connection with the drugs related death of heiress Robin Whitehead. He was one of four people taken into custody after the 27-year-old filmmaker died from a suspected overdose in January at an East London flat.
Whitehead had been making a documentary on Doherty at the time and he previously admitted to visiting the property the day before and the day after she died but on the night of her death he was at his home in Wiltshire.
Doherty, 31, was originally arrested on March 19 on suspicion of supplying drugs then subsequently bailed.
Today, he was handed the lesser charge of possessing the drug, but could still face jail.
A source at the time of Whitehead`s death said: "Pete`s adamant he played no part in Robin`s death. He is still very distressed."
Video footage from Whitehead`s camera showed the Babyshambles star taking crack-cocaine at the home - which was rented by Gill Samworth, 53 - along with his musician friend Peter `Wolfman` Wolfe, 41, who found Whitehead-s body.
Wolfe was today chargedwith two counts of possession of cocaine and one of supplying the Class A drug. The charges against him also relate to Whitehead`s death.
Both Doherty and Wolfe were granted unconditional bail and will appear at Thames magistrates` court on October 18.
Doherty has faced over 20 drugs charges in the past, and also has six convictions for driving offences.