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He will start the role in February — taking over from the retiring Lennox Sharp.
Mr Cooper, who is deputy principal at Oxford Area School, planned to spend the first part of the year getting to know pupils, staff and parents at East Otago.
He graduated from the University of Otago in Science and Zoology and qualified as a secondary teacher at the then Dunedin College of Education.
He wants to see the school increase in size.