Nine years later, Ysgol Gyfun Gymraeg Plasmawr has 800 pupils and top-class results, while Mr Rees won this summer's Royal Air Force teaching award for secondary head of the year in Wales.
His unconventionality was praised by the Plato judges, who called him an "inspirational leader". Tim Austin, the 19-year-old former pupil who nominated him, agrees.
"He's great to talk to and knows every individual child by their first name. Going to school was like meeting friends. There's no truancy because it's such a nice place to go. I miss it."
Mr Rees, 43, grew up near Pontypridd in Welsh-medium schools and read politics, philosophy and economics at Oxford university.
At 21 he taught as a volunteer in a Kenyan school for a year, and decided he liked the adrenalin rush of teaching. A PGCE in business studies ("I knew just enough economics to scrape by") led to work in various south Wales schools while teaching part-time in Cardiff prison for four years.
"Every prisoner is a past pupil of some school, and a percentage of pupils that you teach today are tomorrow's prisoners, so it's not a bad experience," he said.
On Ysgol Plasmawr's opening day in 1998, the young head was matched by a young staff. "Their average age was 27," said Mr Rees. "Their flexibility and lack of cynicism was refreshing."
His biggest challenge as a head has been opening the school in a building he described as "derelict" and the kids called "Sarajevo". The school has now had pound;3 million of new buildings, but still needs sports facilities, technology workshops, and a library.
But an average of 70 per cent of pupils gained at least five A*-Cs at GCSE over the past three years.
Mr Rees says his greatest satisfaction, however, is in individual achievement -the jazz ensemble's national award, a visually impaired pupil in the 2012 Paralympic rowing squad, and a special needs teacher winning a teaching award last year.
Mr Rees, who is married with three teenage children, attributes his own success to high-calibre staff and a supportive governing body. But the wider recognition is welcome, especially for a Welsh-medium school.
"We are so engrossed in producing material and fighting the corner for the survival of our language, we can often be forgotten. We've got one heck of a battle to save this culture."