Johnson was initially arrested on Monday March 2 and was charged after he answered his police bail on Thursday at Peterlee police station.
The charge was confirmed by Durham Police on Thursday afternoon.
The 27-year-old will appear in the magistrates court in Peterlee on May 20.
Johnson’s bail was extended on March 18 which led to Sunderland reviewing the winger’s suspension and allowing him to train pending the outcome of the police investigation.
Gerry Wareham, from the Crown Prosecution Service, revealed he had given police the authorisation to charge Johnson under the Sexual Offences Act 2003.
He said the offences are alleged to have been committed on a single victim between December 30 2014 to February 26 this year.
“May I remind all concerned that the defendant has a right to a fair trial,” Wareham said.
“It is very important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings.
“I would also remind people that the complainant in this case is entitled to lifelong anonymity under the law. For these reasons, it would be inappropriate for me to comment further.”
He joined Sunderland from Manchester City for £10m in August 2012 and scored the winning goal in this season’s Tyne-Wear derby against Newcastle at St James Park.
Born in Sunderland and began his career at Middlesbrough, the winger has played 12 times for England and was initially suspended and then reinstated by his club after being arrested at his mansion in Castle Eden, County Durham.
Sunderland, just a point above the relegation zone in the Premier League, travel to Stoke on Saturday.