Manish Shah, of Brunel Close, Romford, is accused of 65 counts of assault by penetration and 52 counts of sexual assault.
The 47-year-old has also been charged with sexual assault on a child aged under 13 years.
Dr Shah has been released on bail and is due to appear before magistrates in Barkingside on 31 August.
A dedicated phone number for anyone who has concerns or questions has been set up by the NHS - 0800 011 4253.
A doctor from east London has been charged with 118 sexual offences, the Met Police has said.