| Pos | Team | Pld | Pts | GD | W | D | L | F | A |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Brentford | 46 | 85 | +23 | 26 | 7 | 13 | 79 | 56 |
| 2 | Cambridge United | 46 | 81 | +30 | 23 | 12 | 11 | 78 | 48 |
| 3 | Cardiff City | 46 | 80 | +21 | 22 | 14 | 10 | 60 | 39 |
| 4 | Scunthorpe United | 46 | 74 | +11 | 22 | 8 | 16 | 69 | 58 |
| 5 | Rotherham United | 46 | 73 | +18 | 20 | 13 | 13 | 79 | 61 |
| 6 | Leyton Orient | 46 | 72 | +9 | 19 | 15 | 12 | 68 | 59 |
| 7 | Swansea City | 46 | 71 | +8 | 19 | 14 | 13 | 56 | 48 |
| 8 | Mansfield Town | 46 | 67 | +2 | 19 | 10 | 17 | 60 | 58 |
| 9 | Peterborough United | 46 | 66 | +16 | 18 | 12 | 16 | 72 | 56 |
| 10 | Halifax Town | 46 | 66 | +2 | 17 | 15 | 14 | 58 | 56 |
| 11 | 46 | 65 | +11 | 18 | 11 | 17 | 69 | 58 | |
| 12 | Exeter City | 46 | 63 | -3 | 17 | 12 | 17 | 47 | 50 |
| 13 | Plymouth Argyle | 46 | 61 | +4 | 17 | 10 | 19 | 58 | 54 |
| 14 | Chester City | 46 | 57 | -9 | 13 | 18 | 15 | 57 | 66 |
| 15 | Shrewsbury Town | 46 | 56 | -11 | 14 | 14 | 18 | 52 | 63 |
| 16 | 46 | 55 | -17 | 14 | 13 | 19 | 54 | 71 | |
| 17 | Brighton & Hove Albion | 46 | 55 | -17 | 16 | 7 | 23 | 49 | 66 |
| 18 | Southend United | 46 | 54 | -6 | 14 | 12 | 20 | 52 | 58 |
| 19 | Rochdale | 46 | 54 | -13 | 13 | 15 | 18 | 42 | 55 |
| 20 | 46 | 53 | -11 | 12 | 17 | 17 | 47 | 58 | |
| 21 | Hull City | 46 | 53 | -18 | 14 | 11 | 21 | 44 | 62 |
| 22 | 46 | 51 | -13 | 13 | 12 | 21 | 52 | 65 | |
| 23 | Carlisle United | 46 | 49 | -10 | 11 | 16 | 19 | 43 | 53 |
| 24 | 46 | 48 | -27 | 14 | 6 | 26 | 50 | 77 |
Content retrieved from: http://stats.football.co.uk/league_tables/1998_1999/league_two/index.shtml.
