The Warehouse South Dunedin initiated the ban and Pak'n Save and Mitre 10 Mega are considering a similar move.
Any unaccompanied children wearing school uniform, in the store between 8.30am and 3.30pm, will be removed by security staff.
Children in school uniform accompanied by a parent or guardian will not be affected.
The ban is the idea of The Warehouse's senior loss-prevention officer, Rick Butler, who said he had proposed it because of a recent escalation in shoplifting, especially since school started again last week.
The Warehouse staff had detained six children in school uniform last week after shoplifting incidents, he said, and all three businesses regularly experienced problems with young people shoplifting.
"These thefts are getting out of hand. It's got to be stopped. At the moment, it's every second day."
A Pak'n Save spokesman said management were yet to discuss the proposal and declined to comment further.
Mitre 10 Mega loss-prevention supervisor Karl Morris said he supported the "proactive approach" and the store had agreed to explore the initiative.
"We are hoping to get on board."