| Pos | Team | Pld | Pts | GD | W | D | L | F | A |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Swansea City | 46 | 85 | +21 | 24 | 13 | 9 | 51 | 30 |
| 2 | Rotherham United | 46 | 84 | +36 | 24 | 12 | 10 | 72 | 36 |
| 3 | Northampton Town | 46 | 82 | +18 | 25 | 7 | 14 | 63 | 45 |
| 4 | 46 | 79 | +30 | 21 | 16 | 9 | 66 | 36 | |
| 5 | Peterborough United | 46 | 78 | +9 | 22 | 12 | 12 | 63 | 54 |
| 6 | 46 | 75 | +6 | 21 | 12 | 13 | 59 | 53 | |
| 7 | 46 | 72 | +11 | 21 | 9 | 16 | 60 | 49 | |
| 8 | Cheltenham Town | 46 | 70 | +8 | 20 | 10 | 16 | 50 | 42 |
| 9 | 46 | 69 | +10 | 19 | 12 | 15 | 62 | 52 | |
| 10 | Rochdale | 46 | 68 | +3 | 18 | 14 | 14 | 57 | 54 |
| 11 | Brighton & Hove Albion | 46 | 67 | +18 | 17 | 16 | 13 | 64 | 46 |
| 12 | Plymouth Argyle | 46 | 66 | +4 | 16 | 18 | 12 | 55 | 51 |
| 13 | 46 | 65 | +5 | 18 | 11 | 17 | 66 | 61 | |
| 14 | Hull City | 46 | 59 | 0 | 15 | 14 | 17 | 43 | 43 |
| 15 | Lincoln City | 46 | 59 | -2 | 15 | 14 | 17 | 67 | 69 |
| 16 | Southend United | 46 | 56 | -8 | 15 | 11 | 20 | 53 | 61 |
| 17 | Mansfield Town | 46 | 56 | -15 | 16 | 8 | 22 | 50 | 65 |
| 18 | Halifax Town | 46 | 54 | -14 | 15 | 9 | 22 | 44 | 58 |
| 19 | Leyton Orient | 46 | 52 | -5 | 13 | 13 | 20 | 47 | 52 |
| 20 | 46 | 52 | -14 | 12 | 16 | 18 | 39 | 53 | |
| 21 | Exeter City | 46 | 44 | -26 | 11 | 11 | 24 | 46 | 72 |
| 22 | Shrewsbury Town | 46 | 40 | -27 | 9 | 13 | 24 | 40 | 67 |
| 23 | Carlisle United | 46 | 39 | -33 | 9 | 12 | 25 | 42 | 75 |
| 24 | Chester City | 46 | 39 | -35 | 10 | 9 | 27 | 44 | 79 |
Content retrieved from: http://stats.football.co.uk/league_tables/1999_2000/league_two/index.shtml.
