An 11-year-old pupil who was repeatedly raped over two years, allegedly by her stepfather, detailed her pain in letters in a desperate call for help.

According to the girl's aunt, whose name has been withheld to protect the identity of her niece, the minor had written several letters which were allegedly intercepted by her attacker, who destroyed them.

The girl's stepfather, 41, will appear in the Mankweng magistrate's court in Limpopo today.

The aunt found out about the alleged rape and letters after she questioned her niece about taking painkillers on Saturday.

"I was coming from a funeral and feeling very tired. I asked her why she was taking the pills and she bluntly said that her father had raped her and she was in pain," she said.

The girl told her that the suspect would send her other siblings - aged 10 and 7 - to a spaza shop or anywhere far from home before raping her.

The aunt said this has been happening since she was in grade 4. "He would order the young girl into his bedroom and instruct her to undress. He would then rape her. This has been happening since 2017," the woman said.

The aunt said her niece has had "to repeat grade 4 and now she is doing the same with grade 5, repeating".

"She said she was afraid to speak after he once threatened to kill her if she revealed to anyone what was happening."

She added: "I'm hurt and traumatised. He is not a man, he must rot in jail."

She said she was very shocked and had to call an urgent family meeting.

"We called a family meeting after which we went to the police station to open a rape case," she said.

The woman said the mother of the child was too traumatised to speak to Sowetan.

On Tuesday, the girl wrote another letter pleading to travel with her aunt to Gauteng as she would not like to see her stepfather again.

"In the letter, she said, 'My dear aunt, I took a decision to leave with you for Gauteng. I can't live here with my father any more and my mother will go to school and ask for my transfer letter'," the aunt told Sowetan.

Police spokesperson Col Moatshe Ngoepe confirmed the existence of several letters and said they will form part of the evidence.

"The stepfather was arrested around the Mankweng area on Tuesday while on the run," Ngoepe said.

Teddy Bear Clinic spokeswoman Shaheda Omar said many rape survivors may develop psychological trauma that include disruption to emotional, physical and interpersonal behaviour.

"The person starts to isolate themselves and feel sexualised ... also poor performance in school and anxiety," she said.

Women and Men Against Child Abuse director Miranda Friedmann said the rape incident was bound to affect the child's school progress.

"When a rape occurs, a lot of things happen in the mind of the survivor. Many blame themselves for failing to prevent the incident from happening" she said.