The girls aged 11 and 15 were referred after a video allegedly showing a male school pupil being attacked by a girl was published online.
An internet clip apparently showing a schoolgirl, a first-year pupil in Wishaw, North Lanarkshire, attacking a male pupil is understood to have been filmed last night and was posted on YouTube.
It has been removed from the site since it was reported to Strathclyde Police.
A North Lanarkshire Council spokesman said: "The incident happened outwith school hours and away from the school grounds. The incident has been reported to the police who are carrying out investigations.
"Bullying of any kind is not tolerated and our schools have anti-bullying policies and procedures in place."
The two-minute clip allegedly shows the girl, understood to be 11-years-old, facing the boy, who is inches taller than her, before pushing him and punching him repeatedly in the face. It is understood to have happened on Tuesday.
The council spokesman said: "A full school investigation will be carried out and action will be taken."
A police spokeswoman said: "Two girls aged 11 and 15 are being referred to the Children's Reporter in connection with the incident."
The video has been viewed by thousands of people and has sparked anger from furious Facebook and Twitter users.