The burger was removed from the school for testing last week, around the same time frozen mince was taken from school kitchens for DNA testing, which the council said tested negative for horse DNA.
North Lanarkshire council said the Food Standards Agency (FSA) had been informed and investigations are continuing.
A procurement agency called Scotland Excel has advised councils in Scotland to place a “hold on the use of all frozen beef burger products”.
Beef burgers have now been removed from school kitchens in the area and the local council is focusing its investigation on the supply chain over the last three months. The council said three months is the maximum length of time the burgers would be held in storage.
Rural Affairs Secretary Richard Lochhead said: “It is unacceptable that a burger which has tested positive for traces of horsemeat was supplied to a school in North Lanarkshire.
“However, North Lanarkshire council have taken immediate action to withdraw the products from the schools and, as a precautionary measure, all Scottish schools have been advised to put a hold on the use of frozen burgers.”
He added that it was the first positive test result for horse DNA in Scottish schools, but is “one too many”.
“No company should be supplying our schools with food with beef products that contain traces of horsemeat,” he added.
The council said: “ We are working closely with the FSA and Scotland Excel and will continue to take any action necessary to ensure the integrity of foods used in our establishments.”
Are expected to publish more horse DNA test results today as part of the on going investigation into the meat supply chain.