The minor (aged 2), who was living at the Palabek Ogili settlement centre, was recently killed in what is believed to be a ritual killing.
The girl went missing at the centre in Lamwo District on March 21.
Her body was found days later at a swamp with parts such as limbs and genitals missing.
Lamwo police confirmed the suspect, who could not be named as he has not appeared in court, is also from South Sudan.
It is alleged the witch doctor had promised to find the missing girl on condition that he was paid an unspecified amount of money.
However, it emerged he eventually found the body and notified the parents.
“The suspect is being held at Lamwo Central Police Station for questioning,” said a police spokesman.
About 50 000 refugees have fled the civil war in South Sudan and sought safety in the neighbouring Uganda to the south.
– CAJ News