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Gillingham will face West Bromwich Albion’s academy side in the EFL Trophy.
The Gills will also be up against Millwall and Luton in the opening round group stage of the rehashed competition.
The Football League Trophy has undergone radical changes since ending their sponsorship deal with Johnstone’s Paint. The competition is now known as the EFL Trophy.
Gillingham are part of a four-team group – there are 16 groups in total - that controversially consists of one top-graded academy.
Football League teams voted for the new format during their annual conference this summer.
But that vote was based on the academies, such as Liverpool, Manchester United and Arsenal, who have all since declined to take part. A clash with international under-21 matches means the top academy sides are no longer interested in being involved.
Gills chairman Paul Scally was against the idea from the off.
The new EFL Trophy format has received a backlash from supporters, who are angered at the decision to allow top-flight academy teams to enter the trophy, leading to some fan groups threatening to boycott the competition.
Gillingham were part of the 'southern section' draw that involved academy sides from Norwich, Southampton, Brighton and West Brom.
Group stage games that end level after 90 minutes with go to a penalty shootout and the winners will receive an additional point. The top two teams progress to a regional first round proper, consisting of 32 teams.
There is an increased prizefund this year, with the Premier League adding an extra £1m to the pot. Each win will net participating teams £10,000 while there is £5,000 on offer for a draw during the group stage. The eventual winners, in a Wembley final, would net £100,000 in prize money.
Gillingham must field a minimum of five first team players in their starting XI while academy sides must start with six under-21s (as at June 30).
Group stage games take place on week commencing August 29, October 3 and November 7. The schedule has yet to be confirmed.