The Prince's Trust will become the league's official charity until summer 2007, marking the league's first multi-year tie-up in this sector. Previously it rotated its official charity partner on an annual basis.
John Nagle, head of communications at the Football League, described the deal as 'much more than a fundraising exercise'.
He added: 'This partnership fits the themes that underpin the recent rebranding of the Football League, in particular that football clubs are the embodiment of community.'
The Prince's Trust's association with football is part of the charity's overhaul of its image to improve connections with deprived young people.
As part of a brand revamp, it organised the Urban Music Festival at Earl's Court in May.
The league's clubs will offer Prince's Trust members work placements, talks, stadium tours, match tickets and use of club logos in promotional activity.
The charity also has links with the Premier League, grass-roots football charity the Football Foundation and the Professional Footballers' Association.