Courtney went missing on 4 May in Salberau in Elsies River.
Her mother, Juanita Pieters, 42, left her Pluto Street home for work in Epping, leaving Courtney with her seven-year-old brother.
She was last seen standing on the corner of Milky Way and Grandview Avenue at approximately 8am.
A police and community search party stumbled upon body of a child in Bofors Circle Epping Industria at 1.30pm on Saturday afternoon.
Forensics removes the body from an open field in Epping.
Police spokesperson FC van Wyk confirmed the gruesome find.
"As part of an ongoing search for missing three-year-old girl from Elsies River, police and community, volunteers discovered a child's body in Bofors Circle in Epping 2 this afternoon. She was reported missing last week on Thursday," says Van Wyk.
"SAPS crime scene experts and a forensic pathologist were called to the scene. The body has been taken to the mortuary where further tests will be conducted to determine if it is that of missing Courtney Pieters of Elsies River.The provincial FCS continue with the investigation.
"Anyone with any information about this incident is kindly requested to contact the investigating officer Detective Captain Taylor on 082 522 1090."