Players from the European Union will have to go through a points-based system similar to that which currently applies to overseas players before being allowed to play in the Premier League, under new proposals.
The Football Association, Premier League and Home Office will decide on the criteria for such players to obtain a work permit, which could come into force early next year.
The impact on player transfer and movement was described by the FA as "the most significant risk of Brexit".
The points-based system, or Governing Body Endorsement (GBE), is designed to enable the best talents to play in England but put restrictions in place so as not to disadvantage young home-grown players.
Non-EU overseas players are currently graded according to factors such as their transfer fee, proposed wages, the world ranking of their country, the league in which they play and how many minutes they have played for their previous club.
The current rules state that their employment is intended to "make a significant contribution to the development of football at the highest level in England".
BBC Sport understands a meeting will take place next week between the FA and Premier League to discuss the criteria for EU players, which will not necessarily match the current rules for non-EU players.
Ways to enhance opportunities for home-grown players are also expected to be discussed.
The new points-based system would come into force when the UK officially leaves the EU, which is expected to be the start of 2021.
It could come in midway through the season, but the intention is for the measures to have been agreed before the start of the 2020-21 season.
The FA's latest accounts state Brexit could have "a potential negative impact on the number of European players entering the English game which could result in a devaluation of the domestic rights of English competitions".
But the FA says this "could be an opportunity for the English players in the Premier League but also other leagues from English Football League [EFL] to the Barclays FA Women's Super League (WSL)".