Group winners will be drawn at home against a runner-up from another group. In order to achieve this, each draw is split into two sections as detailed below.
Northern Section
Draw A
| Winners Pot | No. | Runner up Pot | No. |
| Everton U21 | 1 | Barnsley | 13 |
| Bolton Wanderers | 2 | Mansfield Town | 14 |
| Port Vale | 3 | Barrow | 15 |
| Salford City | 4 | Bradford City | 16 |
Draw B
| Winners Pot | No. | Runner up Pot | No. |
| Lincoln City | 5 | Morecambe | 9 |
| Grimsby Town | 6 | Tranmere Rovers | 10 |
| Manchester United U21 | 7 | Wolverhampton Wanderers U21 | 11 |
| Burton Albion | 8 | Accrington Stanley | 12 |
Southern Section
Draw A
| Winners Pot | No. | Runner up Pot | No. |
| Colchested United | 1 | Bristol Rovers | 13 |
| AFC Wimbledon | 2 | Newport County | 14 |
| Milton Keynes Dons | 3 | Sutton United | 15 |
| Stevenage | 4 | Arsenal U21 | 16 |
Draw B
| Winners Pot | No. | Runner up Pot | No. |
| Plymouth Argyle | 5 | Charlton Athletic | 9 |
| Forest Green Rovers | 6 | Portsmouth | 10 |
| Chelsea U21 | 7 | Cheltenham Town | 11 |
| Ipswich Town | 8 | Peterborough United | 12 |