Ellery said the student had only been at school for one day, and all close contacts have been approached and are isolating.
"It hasn't had a huge impact," she said.
"We've covered all the classes and allowed people the time to get tested. This is our first time so we are just following everything by the book."
She said the number of students learning from home continued to grow each passing day.
"It's a hell of a time I tell you."
Whanganui Collegiate School and Carlton School have both had positive cases in the last few days.
A teacher from Collegiate was a confirmed case on Tuesday, with no close contacts associated as the teacher hadn't been at school this week.
On Sunday, Carlton School announced one classroom would be closed until Wednesday as a positive case was confirmed for He Puna Oranga Room 11/12.
All pupils in the class have been asked to stay at home, get tested, isolate, and follow the guidelines given in an email that was sent to households.
The school and all other classes remain open and children can attend as normal.
In New Zealand, there were 3297 new cases of Covid-19 announced on Wednesday and 179 people were in the hospital with the virus.
