David Hoare said he had told UK education secretary Justine Greening he was resigning with immediate effect.
The former businessman’s resignation comes just weeks after he was forced to apologise for his comments about the Isle of Wight.
He was widely criticised after being caught on tape at a teaching conference making disparaging remarks about the Isle of Wight.
“Most people go there for sailing for two weeks a year. There’s a sailing club that is one of the best in the world, where there’s champagne,” he said in the recording, obtained by the Times Education Supplement (TES).
“But just within inches, there are people who live in a ghetto ... They think of it as holiday land. But it is shocking. It’s a ghetto; there has been inbreeding.”
He later issued an apology after his comments, reported by the TES.
Mr Hoare also made a telephone call to the leader of Isle of Wight Council, Jonathan Bacon, to make a personal apology, during which he offered to visit the island.