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Archers Court Maths and Computing College head Elaine Hamilton will not be in charge of the new academy when it opens in September.
Richard Williams, head teacher of Medina High School on the Isle of Wight has been given the job instead.
Mrs Hamilton says she wishes everyone connected with the college a very successful future.
The recruitment process was run by the sponsors of the new academy, Canterbury Christ Church University. the Dover grammar schools and Kent County Council.
A spokesman for KCC said the appointment was subject to the closure of Archers Court being approved, and the signing of a funding agreement for the new academy.
“The sponsors have every confidence that Richard Williams will provide successful leadership, enabling the academy to continue to raise academic standards and improve the educational offer for all students."
Mrs Hamilton said: “It has been a pleasure and an honour to lead the school, since June 2002, and as I move on to my third headship, I wish everyone associated with the school an extremely successful future.”
Full story in this week's Dover Mercury.