The agreement will initially televise live League football, Worthington Cup and LDV Trophy games.
The deal will be worth £20m in the first season.
Sky intends to broadcast live matches on Saturday evenings at 5.35pm, along with some games on Friday evening and Sunday afternoons.
The League could also agree a deal for a highlights package.
The deal will see:
The deal brings fresh hope to a number of financially-crippled clubs who were left facing a bleak future after the collapse of the ITV Digital television deal.
The rights reverted to the League after the collapse, and they have now returned to Sky in a deal which will see more than 300 live matches shown between now and the end of the 2005-6 season.
Football League chief executive David Burns said in a statement: "This is great news for the Football League and its clubs.
"This agreement will help to provide financial stability to clubs at a very important time, as well as top-class coverage of our games." Vic Wakeling, managing director of Sky Sports said in a statement: "Sky are delighted to be involved with The Football League and we hope that the clubs can now plan for the future.
The League will press ahead with legal action against the owners of ITV Digital, Carlton and Granada, at the High Court in London on 26 July.