The latest casualty is Tony Garwood, head of East Brighton College of Media Arts, who threw the towel in on Wednesday.
Mr Garwood, who supervised the closure of Marina High school and re-opening of the new school last September, said: "During this year we have begun the process of creating a new college aspiring to high standards. It is my judgement that the college will be best served by appointing a new principal whose skills match closely the key tasks."
The Brighton head follows Torsten Friedag, the pound;70,000-a-year head of the Islington Arts and Media school, north London, who stepped down last Friday after only six months at the former George Orwell School, re-opened under Fresh Start.
Disciplinary problems and truancy are reported to have plagued the school.
The same day, Carole McAlpine resigned after 18 months as head of the first Fresh Start school, Firfield Community School in Newcastle upon Tyne. Sheis leaving at the end of the term to take up a post as director of Great Yarmouth Education Action Zone.
Firfield, formerly Blakelaw school, also faces severe disciplinary difficulties. Teacher morale was also reportedly damaged by the Channel Four documentary filmed in the school.
She defended her decision to leave and added: "I was only ever going to be here in a short-term capacity."
The resignations came only a week after Mr Blunkett urged local authorities to consider expanding Fresh Start - under which schools are closed, refurbished and re-opened under a new name and often with new staff - to schools with three years' bad GCSE results.
John Dunford, general secretary of the Secondary Heads' Association, said:
"Turning around the fortunes of schools in difficult areas is about more than parachuting in so-called superheads.
"The problems these schools find themselves facing are rooted in their local communities. Solutions require a broad approach, where support is given not only to the school but also to the community it serves."