Police said there was no case in 1999 and the council paid him damages in 2002. So why has it taken until now for the GTC to exonerate John Davies?
Sending pupils on cross-country runs may not seem like child abuse. Yet it was one of the accusations against John Davies, who was last week finally allowed to teach again - eight years after he was suspended as a headteacher.
Mr Davies, who turns 59 next month, said he was relieved to clear his name but that it was now too late for him to consider returning to the classroom.
He criticised England's General Teaching Council for taking two years and eight months to conclude a disciplinary hearing when he had already been cleared by the police and won a settlement from Kent council.
"It was going on so long I was worried there would be a posthumous adjudication, because my dad died when he was 64," Mr Davies said. "I lost my job, I lost my career, I lost my home. But please don't paint me as a victim, I'm not crying into my beer."
Mr Davies had spent his entire career in teaching, becoming head of Swinford Manor, a residential school for boys with special needs in Ashford, Kent, in 1989.
The school, whose pupils are aged between 10 and 16, was rated as outstanding by inspectors in 1996 and awarded beacon status in 1998.
But on December 8, 1998, Mr Davies was suspended when police investigated a series of claims by a parent, including that staff beat up pupils and fed them on bread and water.
Although the police called off their investigation, the council carried on with its own, which led to a disciplinary hearing and Mr Davies's dismissal in 2000 for gross misconduct.
Accusations against the head included that he had used innappropriate head-locks on the special needs pupils and had kicked a boy's feet out from under him when he started to cry - claims Mr Davies flatly denied.
"It's not nice to go into Sainsbury's and see front pages of newspapers with your photo on them accusing you of child abuse," he said.
Mr Davies took the council to an industrial tribunal in December 2002 over his dismissal and later won a substantial undisclosed out-of-court settlement.
The former head, who set up a property developing business while waiting to return to teach, had thought his tribulations were over.
"I remember in December 2003 telling my wife what a relief it was going to be to have a Christmas when there wasn't a tribunal or an investigation hanging over us," he said. "Then the next day I get a letter from the GTC."
Mr Davies said that he did not even know what the GTC was when it informed him it was holding a disciplinary hearing. The council was established two years after he was suspended.
The GTC held five days of hearings over the next two years and eight months, cancelling one of the days at short notice because of "staff training".
The panel heard evidence from Ian Craig, assistant director of operations for Kent council, who carried out the council's investigation and accused Mr Davies of infringing pupils' human rights.
He criticised the head's decision to make videos demonstrating restraint techniques, which he likened to breaking in horses. Dr Craig also said that the head's habit of punishing pupils with cross-country runs was a form of child abuse.
Mr Davies insisted the school physically restrained very few pupils, only around 15 a year, and that it meant no pupil had needed to be permanently excluded.
He also defended his habit of sending the boys on runs, saying he had often joined them and that it had been a bonding experience.
Mr Davies told the hearing: "If taking kids for cross-country runs is physical abuse, the GTC has a job for life."
Last week, the GTC committee decided that the allegations of the attacks could not be proven and that Mr Davies had treated complaints about child protection consistently.
They ruled that the restraint techniques did not contravene standard TCI (therapeutic crisis intervention) methods and that the runs were within "a reasonable framework of sanctions".
Mr Davies said he was delighted by the support he had received over the eight years from the National Association of Head Teachers, and praised the panel's judgment. But he criticised the GTC for taking so long to schedule the hearings. The TES revealed this month that the backlog of disciplinary cases has doubled in the last year leaving more than 140 teachers awaiting judgements.
Fiona Johnson, communications director for the GTC, said the council wanted to "deal with disciplinary cases in as timely a way as possible" and was introducing measures to speed up the process, including widening the pool of panel members.
Knee problems mean that Mr Davies has recently had to give up cross-country, but he looks back fondly on the runs and other memories of Swinford Manor. "I worked with some great kids and some super people," he said. "It's just a shame the way it ended."
Ian Poole, who represents NAHT members at the GTC's hearings, said the council had underestimated how many days were needed when it had clearly been a complex case.
"I don't see how anyone could look at a case where a headteacher has had to wait for eight years for an outcome and see it as anything other than appalling," he said.
Kent council was unable to comment.
EIGHT YEARS OF HELL FOR HEAD WHO DENIED 'ABUSE'
September 1989 John Davies becomes head of Swinford Manor school in Ashford, Kent.
February 1996 Swinford Manor is included on Ofsted's list of outstanding schools.
December 1998 Mr Davies is suspended as head after complaints by a parent that pupils are being mistreated.
August 1999 A police investigation concludes that there is no case to answer.
Autumn 1999 Kent education authority launches its own investigation.
July 2000 Local authority disciplinary hearing begins.
October 2000 Mr Davies is dismissed for gross misconduct.
July 2001 Re-hearing of dismissal.
November 2001 Appeal against dismissal denied.
March 2002 Mr Davies takes case to a tribunal, set for January 2003.
December 2002 Kent council pays him an out-of-court settlement.
December 2003 General Teaching Council informs Mr Davies it will carry out a conduct hearing.
September 2005 First GTC hearing.
April 2006 Second hearing, but one of day is cancelled for "staff training".
July 2006Final GTC hearing clears Mr Davies.