| Friday 2nd November 2012 | |||
| Cambridge City | 0-0 | Milton Keynes Dons | |
| Sunday 4th November 2012 | |||
| Burton Albion | 3-3 | Altrincham | |
| Dorchester Town | 1-0 | Plymouth Argyle | |
| Monday 12th November 2012 | |||
| Replay | |||
| AFC Wimbledon | 4-3 | York City | aet |
| Tuesday 13th November 2012 | |||
| Braintree Town | 0-3 | Tranmere Rovers | |
| Replay | |||
| Barrow | 1-0 | Guiseley | |
| Bradford City | 3-3 | Northampton Town | aet |
| (Bradford City won on penalties) | |||
| Milton Keynes Dons | 6-1 | Cambridge City | |
| Nuneaton Town | 0-2 | Luton Town | |
| Rochdale | 0-1 | Morecambe | |
| Slough Town | 1-1 | Mansfield Town | aet |
| (Mansfield Town won on penalties) | |||
| Walsall | 2-3 | Lincoln City | aet |
| Wednesday 14th November 2012 | |||
| Gloucester City | 0-2 | Leyton Orient | |
| Thursday 15th November 2012 | |||
| Replay | |||
| Altrincham | 0-2 | Burton Albion | |










