12th May 2007
| Final | 2-3 | Stevenage |
17th March 2007
| Semi Final 2nd Leg | 3-2 |
| Semi Final 2nd Leg | Stevenage | 2-1 |
10th March 2007
| Semi Final 1st Leg | 2-0 |
| Semi Final 1st Leg | 0-1 | Stevenage |
25th February 2007
| Quarter Final | 1-4 |
24th February 2007
| Quarter Final | Stevenage | 3-0 |
| Quarter Final | 3-0 | Ebbsfleet United |
| Quarter Final | 3-1 | FC Halifax Town |
6th February 2007
| 3rd Round Replay | Stevenage | 3-0 | Morecambe |
| 3rd Round Replay | Braintree Town | 1-3 |
3rd February 2007
| 3rd Round | 1-2 |
| 3rd Round | 2-1 |
| 3rd Round | Ebbsfleet United | 2-1 |
| 3rd Round | 0-0 | Braintree Town |
| 3rd Round | FC Halifax Town | 3-1 |
| 3rd Round | 0-2 |
| 3rd Round | Morecambe | 1-1 | Stevenage |
| 3rd Round | 2-1 |
30th January 2007
| 2nd Round Replay | 2-1 |
23rd January 2007
| 2nd Round | 0-1 |
| 2nd Round | 1-1 |
22nd January 2007
| 2nd Round Replay | 3-1 | Newport County |
16th January 2007
| 2nd Round Replay | 3-1 |
| 2nd Round Replay | FC Halifax Town | 2-1 | Oxford United |
13th January 2007
| 2nd Round | Exeter City | 0-1 |
| 2nd Round | 0-2 | Braintree Town |
| 2nd Round | Ebbsfleet United | 0-1 |
| 2nd Round | Morecambe | 5-0 |
| 2nd Round | Newport County | 0-0 |
| 2nd Round | Oxford United | 2-2 | FC Halifax Town |
| 2nd Round | 3-2 | Dagenham & Redbridge |
| 2nd Round | 2-1 |
| 2nd Round | Stevenage | 3-1 |
| 2nd Round | 0-4 |
| 2nd Round | 0-1 |
| 2nd Round | 2-1 | Burton Albion |
| 2nd Round | 2-0 |
| 1st Round Replay | 2-1 |
| 2nd Round | 1-1 |
9th January 2007
| 1st Round Replay | Oxford United | 1-0 |
6th January 2007
| 1st Round Replay | 0-4 |
19th December 2006
| 1st Round Replay | 2-1 | Harrogate Town |
| 1st Round Replay | 0-1 |
| 1st Round Replay | 0-2 |
| 1st Round | Barrow | 2-5 |
18th December 2006
| 1st Round Replay | 1-2 |
17th December 2006
| 1st Round | 0-1 |
16th December 2006
| 1st Round | Gateshead | 0-4 | Burton Albion |
| 1st Round | Harrogate Town | 1-1 |
| 1st Round | 1-0 |
| 1st Round | Morecambe | 2-1 |
| 1st Round | 3-1 |
| 1st Round | 1-3 |
| 1st Round | Dagenham & Redbridge | 2-0 | Crawley Town |
| 1st Round | 3-2 |
| 1st Round | 0-0 |
| 1st Round | 1-2 |
| 1st Round | 1-0 |
| 1st Round | 3-2 |
| 1st Round | 1-0 |
| 1st Round | 2-2 |
| 1st Round | 0-3 |
| 1st Round | 2-1 |
| 1st Round | 0-0 | Oxford United |
| 1st Round | 4-4 |
| 1st Round | 5-0 | Cambridge United |
| 1st Round | Havant & Waterlooville | 1-2 | Ebbsfleet United |
| 1st Round | 3-1 |
| 1st Round | FC Halifax Town | 3-1 |
| 1st Round | Forest Green Rovers | 0-1 |
| 1st Round | 1-1 |
| 1st Round | 0-0 |
| 1st Round | Aldershot Town | 1-2 |
| 1st Round | Newport County | 2-1 |
| 1st Round | Exeter City | 3-0 |
| 1st Round | Stevenage | 7-0 |
| 1st Round | Braintree Town | 3-0 |