16th April 2000
| Final | Bristol City | 1-2 | Stoke City |
22nd March 2000
| Northern Section Final 2nd Leg | Stoke City | 1-0 |
14th March 2000
| Southern Section Final 2nd Leg | Exeter City | 1-1 | Bristol City |
| Northern Section Final 1st Leg | 1-3 | Stoke City |
7th March 2000
| Northern Section Semi-Final | Carlisle United | 0-1 |
29th February 2000
| Southern Section Final 1st Leg | Bristol City | 4-0 | Exeter City |
22nd February 2000
| Northern Section Quarter-Final | Hartlepool United | 1-2 | Carlisle United |
15th February 2000
| Northern Section Semi-Final | Chesterfield | 0-1 | Stoke City |
| Southern Section Semi-Final | Exeter City | 3-2 | Brentford |
| Southern Section Semi-Final | Bristol City | 4-0 | Reading |
25th January 2000
| Northern Section 2nd Round | Carlisle United | 2-1 | Wigan Athletic |
| Northern Section Quarter-Final | Scunthorpe United | 1-2 | Chesterfield |
| Northern Section Quarter-Final | 0-0 | Hull City |
| Northern Section Quarter-Final | Blackpool | 1-2 | Stoke City |
| Southern Section Quarter-Final | Exeter City | 1-0 |
| Southern Section Quarter-Final | Bristol City | 1-1 | AFC Bournemouth |
| Southern Section Quarter-Final | Brentford | 2-0 | Oxford United |
24th January 2000
| Southern Section Quarter-Final | Bristol Rovers | 1-2 | Reading |
18th January 2000
| Northern Section 2nd Round | Oldham Athletic | 0-1 | Stoke City |
| Southern Section 2nd Round | Barnet | 1-2 | Reading |
12th January 2000
| Southern Section 2nd Round | Bristol City | 3-1 | Cheltenham Town |
11th January 2000
| Southern Section 2nd Round | Oxford United | 1-1 | Wycombe Wanderers |
| Southern Section 2nd Round | Peterborough United | 0-1 | Brentford |
| Southern Section 2nd Round | Plymouth Argyle | 0-1 |
| Southern Section 2nd Round | AFC Bournemouth | 1-0 | Brighton & Hove Albion |
| Northern Section 2nd Round | Hull City | 2-0 |
| Northern Section 2nd Round | Mansfield Town | 0-1 | Blackpool |
| Northern Section 2nd Round | 3-2 | Macclesfield Town |
| Northern Section 2nd Round | Rotherham United | 1-4 | Chesterfield |
| Southern Section 1st Round | Cambridge United | 1-2 | Barnet |
| Southern Section 2nd Round | Exeter City | 2-0 | Swansea City |
| Southern Section 2nd Round | Northampton Town | 0-0 | Bristol Rovers |
10th January 2000
| Northern Section 2nd Round | Preston North End | 1-2 | Hartlepool United |
8th January 2000
| Northern Section 2nd Round | Lincoln City | 1-2 | Scunthorpe United |
8th December 1999
| Southern Section 1st Round | Reading | 1-0 | Leyton Orient |
7th December 1999
| Northern Section 1st Round | Wigan Athletic | 2-1 | Burnley |
| Northern Section 1st Round | Stoke City | 3-2 |
| Northern Section 1st Round | Rotherham United | 2-1 | Shrewsbury Town |
| Northern Section 1st Round | Preston North End | 4-1 | Wrexham |
| Northern Section 1st Round | Notts. County | 0-1 | Blackpool |
| Northern Section 1st Round | Mansfield Town | 2-1 |
| Northern Section 1st Round | Hartlepool United | 1-0 | FC Halifax Town |
| Southern Section 1st Round | Swansea City | 3-1 | Colchester United |
| Southern Section 1st Round | Oxford United | 2-0 | Luton Town |
| Southern Section 1st Round | Northampton Town | 1-0 | Cardiff City |
| Southern Section 1st Round | 0-1 | Cheltenham Town |
| Southern Section 1st Round | 0-3 |
| Southern Section 1st Round | Brighton & Hove Albion | 1-0 | Millwall |
| Northern Section 1st Round | 0-1 | Hull City |