The draw, which took place live on national radio at 12.30 this afternoon, also put the two sides alongside last season’s League Two champions Lincoln City.
The introduction of Premier League youth teams into the EFL Trophy three seasons ago proved controversial, with many supporters around the country voicing their opposition.
Last year Portsmouth won the competition – formerly known as the Checkatrade Trophy – on 5-4 penalties after a 2-2 draw with Sunderland.
New Doncaster boss Darren Moore will be hoping to fare better in the competition than last time out, when they failed to progress from the group stages having lost 3-1 to Newcastle u21s.
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Manchester City u21s were the youth team to progress the furthest last season, losing out at the quarter-final stage in a 2-0 defeat at the Stadium of Light.
Fixture dates are yet to be confirmed, though the group stages will be played on the weeks commencing September 2, October 7 and November 11.