The 48-year-old principal, who doubles as a church pastor in and around Thohoyandou, was arrested last week for allegedly raping a 13-year-old Grade 8 pupil.
He was granted R10,000 bail and his case was postponed to March 27 for trial.
The alleged rape victim completed her Grade 7 last year at the primary school where the accused is the principal.
It is alleged that he raped the girl on the back seat of his car on the road between HaMasia and Vuwani on January 16.
He was arrested after a case of rape against him was opened by the girl's parents soon after doctors at Tshilidzini Hospital examined the girl.
The girl's aunt, whose name cannot be revealed to protect the child's identity as she is under age, said her niece told her the principal had had a sexual relationship with her since last year when she was 12 years old.
"I found five missed calls on her phone and when I asked her who the caller was she wouldn't tell. I then took the phone and checked the number and found that the last call took about seven minutes.
"She later told me that the caller was the principal who was just greeting her.
"But when I took her to the social workers she told them that she had started dating the principal in 2011 while she was in Grade 7.
"She told the social workers that the principal gave her money each time she had sex with him and asked her not to tell anyone about the incident," the aunt said.
The incident has come to light barely a month after five teachers accused of having sex with female pupils at Mahlontebe Secondary School in Sekhukhune were dismissed and chased away from the school by angry parents and pupils.
This was after a Grade 11 pupil smashed the car of her teacher after she allegedly caught him red-handed having sex with her classmate.
The teacher, who was allegedly dating both girls, lured them into sleeping with him in exchange for a pass at the end of the year.
The education department warned yesterday that sleeping with female pupils, irrespective of age or the school the pupil attends, was tantamount to rape.
"Having a romantic relationship with pupils is a dismissible offence and could result into a jail sentence of more than 10 years," Limpopo education MEC Dickson Masemola said.