Michael Lockwood, 64, is accused of six counts of indecent assault and three counts of rape against a girl under 16.
He left the Independent Office for Police Conduct (IOPC) in December after it emerged he was being investigated over a historical allegation.
The nine offences allegedly took place between October 1985 and March 1986, the Crown Prosecution Service said.
Rosemary Ainslie, head of the special crime division at the CPS, said: “After carefully considering all of the evidence provided to us by Humberside Police, we have authorised charges against Michael Lockwood, 64, for nine offences under the Sexual Offences Act 1956.
“Mr Lockwood has been charged with six counts of indecent assault and three offences of rape against a girl under the age of 16, alleged to have been committed during the 1980s.
“The Crown Prosecution Service reminds all concerned that criminal proceedings against Mr Lockwood are active and that he has the right to a fair trial.”
Mr Lockwood is due to appear at Hull Magistrates’ Court on 28 June.
The IOPC said it was aware of the charges, adding: “Mr Lockwood was IOPC director general from 2018 to 2022, but as a Crown appointee, not employed by the IOPC.
“As criminal proceedings are active, we are unable to comment any further.”
He was the first person appointed to lead the the organisation when it replaced the Independent Police Complaints Commission in 2018.
It handles the most serious complaints against police in England and Wales.
Before that, he worked in a range of central and local government roles, including being the chief executive of Harrow Council, in north-west London.
After the Grenfell Tower fire in 2017, Mr Lockwood was asked by a government task force to lead the recovery and remediation work and liaise with the bereaved families and survivors.
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