The Reds faced MK Dons in League One last season before of course Barnsley secured promotion and The Dons were relegated under the guidance of Barnsley legend Danny Wilson.
The Reds drew 0-0 at the National Hockey Stadium and won 2-0 at Oakwell.
The two teams have met before in the League Cup when MK Dons were known as Wimbledon.
In 1988/89 in a two legged tie The Reds lost 2-0 at home and won 1-0 away to lose 2-1 on aggregate.
In the First Round of this year's competition Barnsley knocked out League One Blackpool away. Drawing 2-2 after extra time The Reds triumphed 4-2 on penalties.
MK Dons booked this tie by defeating Championship Colchester 1-0 at home in extra time.
Full draw