DNA from the animals was discovered by Food Standards Agency tests yesterday in cottage pies delivered to 47 schools in Lancashire.
It has now been removed from kitchens and officials say children would only have consumed a 'minute' amount of horse meat.
The news comes as meat samples are being tested across the UK and after beef was removed, as a precaution, from school meals in Staffordshire.
The county council, which provides meals to 87 per cent of its schools, said there was no suggestion there had been a problem with contamination.
In the meantime, pupils were being served other meats such as turkey and 'normal school menus' were likely to return after next week's half-term break, it added.
Two Northern Ireland education boards had also withdrawn beef burgers from school menus over the horsemeat issue.
The North Eastern board joined the South Eastern board on Thursday in withdrawing burgers.
A third education board that had also withdrawn burgers - the Southern board - later reinstated burgers after 'confirmation from suppliers that all meat supplied is from a bovine source'.
Lancashire County Councillor Susie Charles, cabinet member for children and schools, said: "We share the concerns people have about what is clearly a major problem in food supplies across the UK and Europe.
"Because of those concerns we decided to seek extra assurance that our external suppliers were not providing any products containing horse meat DNA, and one of the products has returned a positive result.
"Relatively few schools in Lancashire use this particular product but our priority is to provide absolute assurance that meals contain what the label says - having discovered this one doesn't, we have no hesitation in removing it from menus.
"This does not appear to be a food safety issue but I've no doubt parents will agree we need to take a very firm line with suppliers and it is a credit to our officers that we have been able to quickly identify the problem and take the product off the menus."
England's Local Authority Caterers Association told the BBC it was in touch with the major suppliers of meat to schools to seek reassurances that their products were free from horsemeat DNA.
It added that school meals remained nutritious and healthy and a good alternative to packed lunches.