Sixteen invited under-21 teams will be placed into their respective northern and southern section groups, with the 48 EFL clubs placed into pre-determined groups.
The Millers and Rovers, who have not won a game in Rotherham since 1985, will be placed in Group E alongside Scunthorpe United, meaning that Doncaster will face two derbies in the group stages of the competition. An under-21 side will be added to the group.
Bradford City will compete in Group F alongside Lincoln City and Sunderland, while Sheffield Wednesday and Harrogate Town have been pitted together in Group H with Mansfield Town.
Leeds United under-21s are among the list of invited teams in the northern section alongside fellow under-21s sides from Everton, Leicester City, Liverpool, Manchester City, Manchester United, Newcastle United and Wolverhampton Wanderers.