A Crown Prosecution Service spokesman said it had made the decision to charge Mr Ahmad Khan "after reviewing a file of evidence from Staffordshire Police".
Imran Ahmad Khan, MP for Wakefield in West Yorkshire, denies inappropriately touching the teenager in Staffordshire.
The 47-year-old MP appeared before Westminster magistrates via video-link on Thursday. Reporting restrictions on the case were lifted on Friday.
Currently on unconditional bail, Mr Ahmad Khan’s next court appearance will be on 15th July.
In a statement posted on Twitter, Ahmad Khan said: “It is true that an accusation has been made against me.
“May I make it clear from the outset that the allegation, which is from over 13 years ago, is denied in the strongest terms.
“This matter is deeply distressing to me and I, of course, take it extremely seriously.
“To be accused of doing something I did not do is shocking, destabilising, and traumatic. I am innocent.
“Those, like me, who are falsely accused of such actions are in the difficult position of having to endure damaging and painful speculation until the case is concluded.
“I ask for privacy as I work to clear my name.”
Following the hearing, a spokesperson for the Conservative Party said: "Imran Ahmad Khan has had the whip suspended. As there is an ongoing court case we will not be commenting further."