The girl has been admitted to a hospital and is in a critical condition, police said.
"The minor, who lives with her parents in a slum near the railway station, had gone missing around 11 pm last night. Though her parents carried out a thorough search, they failed to find her," Additional Superintendent of Police (ASP) Rajesh Singh Chandel said.
"However, the minor was found crying near the bridge - Pul Patra - under Aishbagh police station area here this morning by people, who alerted the police," the officer said.
Unidentified accused has been booked under IPC sections 376 (rape) and 363 (kidnap) and under the Protection Of Children from Sexual Offences (POCSO) Act, he said.
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According to the officer, the victim's family had come to Bhopal in search of livelihood from Mahoba in Uttar Pradesh a fortnight ago.
The officer said that the girl, whose father is a Dalit and mother a tribal, was in a state of shock.
"We are trying to talk to her to get information about the accused so that he can be nabbed at the earliest," he said.