The clerk was arrested yesterday, police said, adding that he was also "blackmailing" the girl after making a video of the act.
The matter came to light when the victim was admitted to civil hospital at Ambala after consuming some poisonous substance on April 26, police said.
She narrated the entire story to her mother who reported the matter to the police.
In her complaint given to the police, the girl said that the accused was known to her father, and a day when her parents were away to Delhi, the clerk came to her house and raped her.
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The girl also alleged that on April 19 the accused forcibly took her to a hotel in Mussoorie and again raped her.
As her parents were away, he left her back to home on April 21, the girl alleged in the complaint.
After arresting the accused, police produced him before a local court today which remanded him in police custody for two days.