Free state police have arrested a pastor in connection with a 13-year-old girl's rape.

The 37-year-old pastor allegedly told the "problematic" teenager's parents to send her to his residence for a ritual.

Spokesperson Warrant Officer Malebo Khosana said: "This was arranged in order for the pastor to sort her bad behaviour, which includes being naughty and absconding from school".

He said the girl and her 8-year-old brother were sent to the pastor's house at about 2pm on Tuesday.

The pastor allegedly told the brother to go home.

"When the girl entered the house the pastor allegedly undressed her and performed a bathing ritual on her. After that he raped her on the floor," Khosana said.

The girl went home and told her brother about her ordeal. He in turn told their mother.

The girl's mother called the pastor to their home and also alerted the police.

"Police arrested the pastor at the victim's home," Khosana said.

He said Thabong SAPS Family Violence, Child Protection and Sexual Offences Unit were investigating a case of rape.

The pastor is expected to appear at Welkom magistrate's court today.