Three-year-old Courtney Pieters was raped twice before she was killed and buried in a shallow grave.
According to the National Prosecuting Authority (NPA), Courtney was the 19th child murdered in the Western Cape this year.
On Wednesday, Mortimer Saunders, 40, who is believed to have lived with the Pieters family, faced angry members of the public when he appeared in the Goodwood Magistrate's Court on charges of murder and rape.
Prosecutor Anderaan Gelderblom said Saunders was being charged with two counts of rape.
It was Saunders' first appearance after he was arrested on Sunday evening.
On Monday, News24 learnt that Saunders had rented a space in the Pieters' family home.
Saunders, wearing a red T-shirt, entered the dock with his head bowed down, before fixing his gaze on the magistrate.
There was a strong police presence, with about 20 officers maintaining order.
At least 10 officers formed a line between Saunders and the public gallery.
Defence attorney Collin Lukay said his client had no intention of applying for bail, but said an application might be brought at a later stage.
Lukay requested that Saunders be kept in a hospital, instead of prison, for his personal safety.
"On instruction from my client, he asks to be detained at a section of a hospital, and not in prison, as he fears for his life," Lukay said.
Lukay said Saunders did not qualify for legal aid as he scored high in the means test. Saunders is a worker at a call centre, Lukay said.
"My client intends to appeal the means test, as he cannot afford a private defence lawyer," he said.
The courtroom was filled to capacity, with several members of the public and the media seated on the courtroom floor.
Before proceedings started, Magistrate Paul Visagie warned the public that he would not allow any disruptions in his courtroom.
The atmosphere in the courtroom was tense, with police refusing to allow additional people into the already packed room.
Joanie Fredrick, from the Mitchells Plain crisis forum, asked the public to stay silent.
"Can't you see Courtney's parents are here? How difficult do you think this must be for them," Fredricks said loudly.
Pieters' parents asked the media not to photograph them.
They quickly left the court as soon as proceedings ended. The case was postponed to May 24.
Outside the court, more than 100 members of the public held up placards which called for an end to violence against women.
"Restore the death penalty today," one placard read.
NPA spokesperson Eric Ntabazalila said he wished that cases like this didn't have to come to court, because "by this stage, there is already a victim".
"From January up to today... there are 19 children that have been killed in the Western Cape... It is a sad situation we find ourselves in," he said.
Courtney was last seen playing outside her home in Elsies River on May 4. Her body was found on Saturday in a shallow grave next to unused railway tracks in the Epping Industrial area, roughly 2km from her home.
Daniel Dekker, from the Ruyterwacht community watch, told News24 that he had been involved in the search for Courtney from the first day.
"We walked by foot to look for her. We looked everywhere, except Epping. On Saturday, we started looking in Epping when a constable found her," he said.
Asked how he felt during the search, he said: "All I can remember is how angry I was."