The Government is backing the plan, which will help to identify young players and fans who have been sexually abused. There have been fears that some coaches working with juniors have exploited their positions of trust to prey on them.
The screening programme will include every club in the country. Even famous names such as Liam Brady and Steve Heighway, the heads of the football academies at Arsenal and Liverpool, will have to be checked.
As part of a new Child Safe programme, which is launched nationally in Bristol tomorrow, professional footballers are also to be given training in identifying abused young fans who may come to them or write to them for help.
The programme has been developed by Bristol Rovers Football Club and has the support of Tony Banks, the Sports minister, and the Football Association, which hopes it will be adopted by all clubs.
Peter Cates, the FA Premier League's education officer, said: "Football certainly is not complacent about this and is more than aware that any job working with children offers opportunities to people whose motives might not be 100 per cent [honourable]."
The football establishment has been concerned by a series of cases involving the abuse of young players by professional coaches. Last November, Jim Torbett, the founder of Celtic Boys Club, which supplied young players to the famous Glasgow club, was jailed for two years for abusing three teenagers, including Alan Brazil, who later became a Scottish international.
Sheriff Margaret Gimblett told Torbett, a 51-year-old millionaire businessman: "These children were football-mad with stars in their eyes, and perhaps hoping to kick their way to the stars. You knew that, and you betrayed that trust."
Last June, Barry Bennell, 44, who was once employed by Crewe Alexandra and who had a close association with Stoke City and Manchester City in the 1980s, was jailed for nine years for preying on young players.
Chester Crown Court was told that from 1978 to 1992, Bennell talent- spotted boys aged 9 to 14 around the North-west and Midlands before selecting them for junior football teams.
He would invite them to stay with him at his home or take them on tours to various places, including North Wales and Spain, where he sexually abused them.
The FA's response to the problem was developed by the caretaker England coach Howard Wilkinson, who was asked by football bosses to draw up a Charter for Quality, to help clubs to develop their young footballing talent.
The charter, published last April, included a commitment to child protection. Next month, the FA will put this into practice by starting a training programme for all coaches working with young players at the Centres of Excellence and Football Academies that are now attached to professional clubs.
The scheme is principally aimed at helping coaches to identify abused youngsters and put them in contact with specialists from social services and the National Society for the Prevention of Cruelty to Children. But coaches will also be asked to declare criminal convictions on self-certification forms, which will be subject to screening by police.
The FA hopes clubs will go even further and follow Bristol Rovers in adopting a Child Safe scheme, which has been drawn up on police advice. Bristol Rovers has appointed a child protection officer, former teacher Rod Wesson, to oversee the strategy.
Mr Wesson said: "We want to reassure parents who allow their kids to come to us that we have done everything we can to provide them with a safe environment."
The scheme is jointly run with Avon and Somerset Police and has also been adopted by Bath Rugby Football Club and Gloucestershire County Cricket Club.
David Niven, director of the charity Action on Child Exploitation, said: "We hope the big clubs will help this message to cascade down throughout the sports. Abuse can occur at all levels, from kick-abouts in the park to Premier League clubs."