Clubs from steps five, six and seven of the league pyramid will be able to bid for 16 individual grants of £50,000 over the next two years under the scheme, which is being sponsored by Budweiser.
The idea behind the campaign, called Budweiser Club Futures, is to give run-down and semi-professional clubs money to improve their facilities.
Eight grants will be available during the 2012-13 season and eight more will be granted the following season. One of the eight clubs from each season then could receive a further £100,000 "super grant" if they win a Facebook vote which will ask fans to gauge how much impact the funding has had on their facilities.
Sir Trevor Brooking, the FA's director of football development, said: "This £1million investment as part of the Budweiser Club Futures programme is a fantastic gesture, with the £100,000 super grant being a real pot of gold for the clubs involved."
Clubs can apply for the scheme via the FA's website. Applications close on October 31.
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