Mr Fyfe said it had been a privilege to lead Eskdale School over the past four years.
"The students and staff have been a joy to work with," he said.
"The plans for both schools going forward are incredibly exciting.
“Thank you to our parents and the local community for making me feel so welcome.
"I wish you all the best”.
Chair of governors Pen Cruz said: “Andy has shown enormous dedication and hard work in adapting Eskdale to the demands of being an 11 to 16 school.
"He has also worked tirelessly to equip Eskdale to deal with the pandemic and to ensure that staff and students were kept safe.”
Amanda Newbold, Assistant Director for Education and Skills, said: “We are supporting the school’s governors and the federation to ensure robust leadership arrangements will be in place following Andy's departure.
"Interim arrangements will be put in place to ensure there is minimal disruption to pupils’ education or wellbeing in school.
“The Chair of Governors, Pen Cruz, has indicated she will be stepping down from the governing body in February, following the recruitment campaign for executive leadership of the federation.
“Pen has worked tirelessly to support the school and education in Whitby and we would like to thank both leaders for their hard work and dedication over the past years.”