| Pos | Club | P | W | D | L | GF | GA | GD | Pts | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Swansea City | 46 | 24 | 13 | 9 | 51 | 30 | 21 | 85 | pr |
| 2 | Rotherham United | 46 | 24 | 12 | 10 | 72 | 36 | 36 | 84 | pr |
| 3 | Northampton Town | 46 | 25 | 7 | 14 | 63 | 45 | 18 | 82 | pr |
| 4 | Darlington | 46 | 21 | 16 | 9 | 66 | 36 | 30 | 79 | pl |
| 5 | Peterborough United | 46 | 22 | 12 | 12 | 63 | 54 | 9 | 78 | ppl |
| 6 | Barnet | 46 | 21 | 12 | 13 | 59 | 53 | 6 | 75 | pl |
| 7 | Hartlepool United | 46 | 21 | 9 | 16 | 60 | 49 | 11 | 72 | pl |
| 8 | Cheltenham Town | 46 | 20 | 10 | 16 | 50 | 42 | 8 | 70 | |
| 9 | Torquay United | 46 | 19 | 12 | 15 | 62 | 52 | 10 | 69 | |
| 10 | Rochdale | 46 | 18 | 14 | 14 | 57 | 54 | 3 | 68 | |
| 11 | Brighton + Hove Albion | 46 | 17 | 16 | 13 | 64 | 46 | 18 | 67 | |
| 12 | Plymouth Argyle | 46 | 16 | 18 | 12 | 55 | 51 | 4 | 66 | |
| 13 | Macclesfield Town | 46 | 18 | 11 | 17 | 66 | 61 | 5 | 65 | |
| 14 | Hull City | 46 | 15 | 14 | 17 | 43 | 43 | 0 | 59 | |
| 15 | Lincoln City | 46 | 15 | 14 | 17 | 67 | 69 | -2 | 59 | |
| 16 | Southend United | 46 | 15 | 11 | 20 | 53 | 61 | -8 | 56 | |
| 17 | Mansfield Town | 46 | 16 | 8 | 22 | 50 | 65 | -15 | 56 | |
| 18 | Halifax Town | 46 | 15 | 9 | 22 | 44 | 58 | -14 | 54 | |
| 19 | Leyton Orient | 46 | 13 | 13 | 20 | 47 | 52 | -5 | 52 | |
| 20 | York City | 46 | 12 | 16 | 18 | 39 | 53 | -14 | 52 | |
| 21 | Exeter City | 46 | 11 | 11 | 24 | 46 | 72 | -26 | 44 | |
| 22 | Shrewsbury Town | 46 | 9 | 13 | 24 | 40 | 67 | -27 | 40 | |
| 23 | Carlisle United | 46 | 9 | 12 | 25 | 42 | 75 | -33 | 39 | |
| 24 | Chester City | 46 | 10 | 9 | 27 | 44 | 79 | -35 | 39 | r |
| Date | Opponent | Score | Att. | ||||
|---|---|---|---|---|---|---|---|
| 13 July 1999 | Away | Gravesend + North. | Friendly | 1–4 | L | 0 | → |
| 16 July 1999 | Home | Norwich City | Friendly | 2–1 | W | 0 | → |
| 20 July 1999 | Away | Billericay Town | Friendly | 3–1 | W | 0 | → |
| 21 July 1999 | Away | Purfleet | Friendly | 2–0 | W | 0 | → |
| 24 July 1999 | Home | Peterborough Utd | Friendly | 1–1 | D | 0 | → |
| 25 July 1999 | Home | Colchester United | Friendly | 1–2 | L | 0 | → |
| 29 July 1999 | Home | Southend Supporters | Friendly | 7–1 | W | 0 | → |
| 31 July 1999 | Home | Crystal Palace | Friendly | 4–0 | W | 0 | → |
| 7 August 1999 | Home | Plymouth Argyle | League | 2–1 | W | 4981 | → |
| 10 August 1999 | Home | Oxford Utd | League Cup | 0–2 | L | 2618 | → |
| 14 August 1999 | Away | Rochdale | League | 0–2 | L | 2253 | → |
| 21 August 1999 | Home | Mansfield Town | League | 1–0 | W | 3533 | → |
| 24 August 1999 | Away | Oxford Utd | League Cup | 0–1 | L | 4162 | → |
| 28 August 1999 | Away | Swansea City | League | 1–3 | L | 4757 | → |
| 30 August 1999 | Home | Leyton Orient | League | 1–1 | D | 5980 | → |
| 4 September 1999 | Away | Hartlepool United | League | 2–1 | W | 1980 | → |
| 11 September 1999 | Away | Macclesfield Town | League | 2–1 | W | 2059 | → |
| 18 September 1999 | Home | Halifax Town | League | 4–1 | W | 4533 | → |
| 25 September 1999 | Home | Peterborough Utd | League | 0–1 | L | 6187 | → |
| 2 October 1999 | Away | Carlisle United | League | 1–1 | D | 2800 | → |
| 9 October 1999 | Away | Cheltenham | League | 1–2 | L | 3118 | → |
| 16 October 1999 | Home | Shrewsbury Town | League | 3–2 | W | 3963 | → |
| 19 October 1999 | Home | Lincoln City | League | 2–2 | D | 3556 | → |
| 23 October 1999 | Away | Peterborough Utd | League | 0–1 | L | 5860 | → |
| 30 October 1999 | Away | Torquay United | FA Cup | 0–1 | L | 2520 | → |
| 2 November 1999 | Home | Brighton + H.A. | League | 2–1 | W | 4927 | → |
| 6 November 1999 | Away | Exeter City | League | 1–0 | W | 2353 | → |
| 12 November 1999 | Home | Hull City | League | 1–2 | L | 4940 | → |
| 23 November 1999 | Away | Chester City | League | 0–0 | D | 1906 | → |
| 27 November 1999 | Home | Darlington | League | 1–2 | L | 4134 | → |
| 4 December 1999 | Away | Plymouth Argyle | League | 1–3 | L | 4679 | → |
| 7 December 1999 | Home | Cheltenham | Trophy | 0–1 | L | 1227 | → |
| 10 December 1999 | Home | Barnet | League | 1–3 | L | 3521 | → |
| 17 December 1999 | Away | York City | League | 2–2 | D | 2233 | → |
| 26 December 1999 | Home | Northampton Town | League | 2–2 | D | 5449 | → |
| 28 December 1999 | Away | Torquay United | League | 1–0 | W | 3138 | → |
| 3 January 2000 | Home | Rotherham United | League | 1–2 | L | 4788 | → |
| 8 January 2000 | Away | Barnet | League | 1–2 | L | 3057 | → |
| 15 January 2000 | Home | Rochdale | League | 3–3 | D | 3190 | → |
| 22 January 2000 | Away | Mansfield Town | League | 1–3 | L | 2215 | → |
| 29 January 2000 | Home | Swansea City | League | 2–1 | W | 3860 | → |
| 5 February 2000 | Away | Leyton Orient | League | 1–2 | L | 5972 | → |
| 12 February 2000 | Home | Hartlepool United | League | 2–1 | W | 3337 | → |
| 19 February 2000 | Away | Darlington | League | 0–1 | L | 4391 | → |
| 26 February 2000 | Away | Halifax Town | League | 0–0 | D | 2068 | → |
| 3 March 2000 | Home | Macclesfield Town | League | 1–0 | W | 3725 | → |
| 7 March 2000 | Home | Exeter City | League | 1–2 | L | 3122 | → |
| 11 March 2000 | Away | Brighton + H.A. | League | 0–1 | L | 5844 | → |
| 18 March 2000 | Home | Chester City | League | 3–1 | W | 3483 | → |
| 21 March 2000 | Away | Hull City | League | 0–0 | D | 4150 | → |
| 25 March 2000 | Away | Northampton Town | League | 0–2 | L | 5426 | → |
| 1 April 2000 | Home | York City | League | 0–0 | D | 3364 | → |
| 8 April 2000 | Away | Rotherham United | League | 0–0 | D | 4327 | → |
| 22 April 2000 | Away | Shrewsbury Town | League | 1–2 | L | 3540 | → |
| 24 April 2000 | Home | Carlisle United | League | 2–0 | W | 3053 | → |
| 29 April 2000 | Away | Lincoln City | League | 0–1 | L | 2556 | → |
| 2 May 2000 | Home | Torquay United | League | 0–2 | L | 2563 | → |
| 6 May 2000 | Home | Cheltenham | League | 2–1 | W | 4977 | → |