ER24 paramedics said they reported to the school on Tuesday after receiving reports that the pupils were nauseous and vomiting.
When the children got to hospital, however, it was found that only eight of them needed treatment.
"All the children were thoroughly examined by physicians and declared healthy and bug-free, with no traces of food poisoning," said the school.
"However, eight of the 46 appeared to suffer from stomach ailments but were treated and released with the rest of the children."
Northern Academy, an independent school that also offers boarding facilities, said it wanted to ensure the public that it prioritised the safety of its learners.