Parents at Smestow Academy in Wolverhampton were sent a letter from chairman of governors Mike Rickhuss informing them that Clive Jones had left the school.
Mr Rickhuss said Mr Jones' deputy Mrs J Dickens would stand in as acting headteacher until a permanent appointment was made.
His letter said: "We understand that this may come as a surprise to parents and the community, but I am sure you would want to join us in sharing our thanks and best wishes for the future of Mr Jones.
"The senior leadership team and staff will continue to drive the journey to good for all our students and remain focused and determined to ensure that Smestow values remain at the heart of the community."
Mr Jones was appointed executive headteacher in the summer of 2019, following a critical Ofsted inspection.
At the same time, James Till was appointed to replace Angie Lawrence as headteacher in charge of the school's day-to-day running, and Mr Jones also took over this role following Mr Till's departure.
In a September interview, Mr Jones spoke of the progress that had been made at Smestow since its scathing Ofsted report in 2019.
Inspectors said the standard of teaching was "not good enough", and that the school "required improvement" in all five areas it was assessed on. Staff turnover, poor performance of pupils from difficult backgrounds and disruption in class were among the weaknesses highlighted.
But he said an interim report this year found the school had made considerable improvement, and was on course to receive a 'good' rating at its next full inspection.
He said: "I enjoy trying to improve challenging schools, I don't think it's always really recognised.
"If you're the head of an 'outstanding' school, everybody can see what you do, but I think it's really important to help schools by supporting them and developing them.
"We have fantastic students who deserve the best we can possibly give them."
The school, in Windmill Crescent, Castlecroft, is part of the University of Wolverhampton Multi-Academy Trust, which runs 11 other schools including Wednesfield High, Featherstone Academy, Woodhouse Primary Academy in Quinton, Edgar Stammers Primary Academy in Walsall, and Pye Green Academy in Hednesford.