Philip Slater has worked at Le Rocquier for 17 years, initially as deputy head, and is due to leave at Christmas.
A recruitment process is now under way to find his successor and one of the current deputy heads, Sam Baglin, will take over in the meantime as acting head.
Mr Slater said: ‘I am immensely proud of Le Rocquier and all of its achievements. The school has been part of my life for nearly two decades and I have enjoyed every single day. It has a real caring, family atmosphere and it has been an honour to have led the school.
‘My wife has recently retired and my youngest daughter has moved to Australia, so the time has come for me to start the next chapter of my life.
‘It has been a very difficult decision to make and I will miss the school immensely. However, I am more than confident the school is in good hands and I am sure it will go from strength to strength in the future.
‘I would like to take this opportunity of thanking all the students and staff and the wider school community for all of their support over the past 17 years.’
Education Minister Rod Bryans said: ‘Mr Slater has served Jersey’s young people for many years and was part of the team that moved from the old buildings to the new school in 2006.
‘He has always been a great advocate for his school and his staff and I thank him on behalf of the Island for his dedication and his contribution to education.’