Clubs voted for the new levy, set at one per cent, at an EGM at Leicester City's King Power Stadium.
Money raised will be used to help fund youth programmes across the 72 clubs. The League estimate the tax will raise £600,000 a season.
Members have also voted to increase the number of homegrown players (someone who was at a British club for at least three years prior to the age of 21) that must be in a squad to six, an increase of two.
This comes a day after the number of substitutes was cut from seven to five, giving a matchday squad of 16.
The Football League's head of youth development, David Wetherall, said: "Youth development at Football League clubs is one of the games’ success stories, not only in terms of the number of players coming through, but also because our clubs are actually giving these players the chance to show their talent at first-team level.
“Last season alone, 250 young players made their league debut and more than 900 players under the age of 21 appeared in first-team football.
“These initiatives will further strengthen the outstanding work being done by Youth Development staff at clubs throughout The Football League and help even more young players make the step-up into first-team football.”