The footage shared widely on sites like YouTube, Facebook and Twitter shows a man said to be Osama Mohamed Othman hitting the children with a stick and kicking them as they ran away, screaming in pain.
State-run Al-Ahram newspaper said Othman's estranged wife filmed the video two months ago.
"He used to beat the children and that's why I filmed him and uploaded it online in order to expose him," Elham Eid Awad was quoted as saying.
The prosecution said it had referred Othman to trial, and that he could be jailed for three years if found guilty.
Security officials said Othman had been charged with "torturing " 13 children at the orphanage.
The prosecution said some children had accused Othman of beating them for failing to seek his permission to watch television.
Mohamed Faruk, a senior Cairo security official, said on television that during questioning, Othman justified his actions by saying he had been trying to teach the children "a lesson" as they were playing with electrical devices and he feared for their lives.
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