The ex-officer, who shot Azelle Rodney in 2005 after opening fire within a second of pulling up next to the car in which he was travelling, has been identified only as E7 after being granted anonymity during a public inquiry into the 24-year-old's death.
Mr Rodney's mother Susan Alexander said: "I am very pleased at the CPS's decision to prosecute the officer who killed my son. I have waited a long time to see this day and hope this prosecution will lead to justice for Azelle."
The 24-year-old died in Edgware, north London, after officers stopped the car in which he was travelling with two other men, fearing they were on their way to rob Colombian drug dealers and had a sub-machine gun.
Mr Rodney was hit six times: once in each arm and in the back, and fatally four times in the head.
The officer will appear at Westminster Magistrates' Court on September 10.
Director of Public Prosecutions Alison Saunders said: "The decision to prosecute was taken in accordance with the Code for Crown Prosecutors. We have determined that there is a realistic prospect of conviction and that a prosecution is in the public interest."
In recent years there have only been a handful of cases where police officers have been charged with murder while on active duty.
The three-month public inquiry into Mr Rodney's death, chaired by former judge Sir Christopher Holland, found his killing was not justified.
Scotland Yard would not comment specifically on the case, but stressed its marksmen rarely fire their guns.
"Our officers are highly-trained and professional and fire shots only once or twice a year," the force said. "We accept that where this happens, our officers will be subject to detailed scrutiny."