The partnership, called "a season saving men’s lives", will see players, staff and fans of the 72 league clubs raise money for the prostate cancer charity.
Luther Blissett, the former England, Watford and AC Milan footballer, launched the campaign today with David Annand, a supporter of the charity who was diagnosed with the disease last year aged 49.
Annand is walking 500 miles around football grounds across the UK to raise awareness of the disease.
A spokeswoman for Prostate Cancer UK would not say how much the charity hoped to raise through the partnership. The Football League’s partnership with Marie Curie Cancer Care raised £400,000 in 2010. Last year's partnership with Help the Hospices has raised about £170,000 so far, but the final figure is likely to be much higher because clubs gave money directly to their local hospices, a spokeswoman for Help the Hospices said.
Owen Sharp, chief executive of the Prostate Cancer UK, said: "We hope that everyone who comes through the turnstiles this season will get behind the partnership to raise as much as possible and make an even bigger difference to the 250,000 men affected by the disease throughout the UK."
Greg Clarke, chair of the Football League, said: "I would encourage fans up and down the country to get involved with fundraising at their local league club to help fight this disease."