League One and Two clubs have voted to retain invited under-21 teams in the Checkatrade Trophy for two more seasons, along with a increase in prize money and changes to selection rules.
In a one-season trial, 16 Premier League and Championship under-21 sides were added to the 2016-17 tournament.
Clubs voted on three options: keeping academy teams, reverting to the old 48-team format or ending the competition.
Two-thirds of clubs lent their support to the 64-team format.
Coventry City won this season's EFL Trophy in front of nearly 75,000 spectators at Wembley in April, although the early rounds of the competition were greeted by fan boycotts and low attendances.
Luton manager Nathan Jones, who was critical of this season's team selection criteria, has said he is "pleased our feedback has been taken on board".
Jones continued: "Just as importantly though, the EFL have assured clubs that it isn't the thin end of the wedge in terms of Premier League clubs being able to enter B teams into the league.
"I know our supporter groups have been consulted all the way through by the club's board when giving our views, and hopefully any fears they had on that front have been allayed."
A key reason behind the change was to give young players a chance to play competitive fixtures and 27% of players who started EFL Trophy matches in 2016-17 were English under-21s, up from 23% in 2015-16, and 18% in 2014-15.
What are the changes?
Some League One and Two clubs were fined this season for fielding "weakened teams", but changes have been made to allow for greater selection flexibility for clubs.
Third-tier and fourth-tier clubs are now able to choose any goalkeeper and only four starting outfield players now have to be "qualifying first-team players", while invited sides need to have six under-21 players in their starting line-up.
Furthermore, the prize money for the competition has increased from just under £2m to £3m - the bulk of which comes from the Premier League - and regionalisation of the competition will remain until the quarter-final stages.
Invited teams will also play all of their group matches away from home - avoiding scenes such as 274 fans attending The Hawthorns to watch West Bromwich Albion's Under-21 side take on League One Gillingham.
There has been no guarantee from the Premier League clubs who refused to participate this season - including Arsenal, Tottenham, Manchester United, Manchester City and Liverpool - that they will be involved next season.
However, the English Football League hope the flexibility of being able to schedule matches outside international windows will make the proposition more attractive.
'Revised format benefits all parties'
EFL chief executive Shaun Harvey: "We wanted to ensure that League One and League Two clubs had the opportunity to make the key decisions regarding where we take the competition in 2017-18 and beyond, and I believe we have reached a revised format that benefits all parties.
"EFL clubs will have greater flexibility with regard to team selection, while still maintaining the principle that this is a first-team competition for our clubs that will support the development and progression of young players.
"The competition will also provide significant financial rewards for all EFL clubs, which increases with success."
Simon Stone, BBC Sport
There is no doubt the additional £1m prize money has played a big part in this competition continuing.
Derided by fans - and some clubs, the tournament has been saved by the Premier League offering additional funds, proving, in a week when Accrington have questioned their involvement in the lower league, just how important their financial input actually is.
However, whilst the concept of providing a competitive platform for England's best young players is one for which the EFL should be applauded, the best has to mean the best.
Arsenal, Manchester City, Manchester United, Tottenham and Liverpool opted not to take part last season.
For there to be any point to the Checkatrade Trophy in its revised form, they need to be involved next term.