The five-year-old was abducted in the wee hours from the porch of her house while she was sleeping with her parents from Jodhpuria Basti in Jhunjhunu district.
The mother was shocked to find her daughter missing when she woke up at around 1.30 am, said the police.
After a complaint was lodged, the police found the girl at the Mandawa road.
"She was unconscious and was rushed to the government hospital. Later, based on the statement of the victim, we arrested a youth identified as Mahesh on the charges of kidnapping and raping the girl," said superintendent of police, Shivlal Joshi.
The accused youth has been arrested and booked under Sections 384 and 376 of Indian Penal Code.