Statistics of League of Ireland in the 1998–99 season.
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The Premier Division was contested by 12 teams and St Patrick's Athletic F.C. won the championship.
The First Division was contested by 10 teams and Drogheda United F.C. won the division.
| Pos | Club | Pts | W | D | L | GF | GA | GD | |
| 1 | St Patrick's Athletic F.C. | 73 | 22 | 7 | 4 | 58 | 21 | +37 | |
| 2 | Cork City F.C. | 70 | 21 | 7 | 5 | 62 | 25 | +37 | |
| 3 | Shelbourne F.C. | 47 | 13 | 8 | 12 | 37 | 35 | +2 | |
| 4 | Finn Harps F.C. | 46 | 12 | 10 | 11 | 39 | 40 | -1 | |
| 5 | Derry City F.C. | 45 | 12 | 9 | 12 | 34 | 32 | +2 | |
| 6 | University College Dublin A.F.C. | 42 | 10 | 12 | 11 | 31 | 32 | -1 | |
| 7 | Waterford United F.C. | 42 | 11 | 9 | 13 | 21 | 37 | -16 | |
| 8 | Shamrock Rovers F.C. | 40 | 9 | 13 | 11 | 34 | 40 | -6 | |
| 9 | Sligo Rovers F.C. | 38 | 9 | 11 | 13 | 37 | 50 | -13 | |
| 10 | Bohemian F.C. | 37 | 10 | 7 | 16 | 28 | 37 | -9 | Play-off(Won) |
| 11 | Bray Wanderers A.F.C. | 32 | 8 | 8 | 17 | 30 | 45 | -15 | Relegated |
| 12 | Dundalk F.C. | 27 | 6 | 9 | 18 | 23 | 40 | -17 | Relegated |
| Pos | Club | Pts | W | D | L | GF | GA | GD | |
| 1 | Drogheda United F.C. | 64 | 17 | 13 | 6 | 57 | 32 | +25 | Promoted |
| 2 | Galway United F.C. | 64 | 16 | 16 | 4 | 53 | 34 | +19 | Promoted |
| 3 | Cobh Ramblers F.C. | 58 | 17 | 7 | 12 | 55 | 43 | +12 | Play-off(Lost) |
| 4 | Longford Town F.C. | 54 | 15 | 9 | 12 | 41 | 33 | +8 | |
| 5 | Kilkenny City A.F.C. | 53 | 14 | 11 | 11 | 49 | 46 | +3 | |
| 6 | Limerick F.C. | 52 | 13 | 13 | 10 | 39 | 35 | +4 | |
| 7 | Monaghan United F.C. | 44 | 10 | 14 | 12 | 44 | 44 | 0 | |
| 8 | Athlone Town A.F.C. | 40 | 10 | 10 | 16 | 45 | 61 | -16 | |
| 9 | Home Farm Everton F.C.* | 38 | 11 | 5 | 20 | 42 | 54 | -12 | |
| 10 | St Francis F.C. | 18 | 2 | 12 | 22 | 25 | 68 | -43 |
'*'Home Farm Everton F.C. changed their club name to Home Farm Fingal F.C. for next season.
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