| Season | 1998-99 |
|---|---|
| Champions | Anorthosis 10th championship |
| Relegated | Evagoras Paphos Doxa Katokopia Aris |
| Champions League | Anorthosis (2nd qualifying round) |
| UEFA Cup | AC Omonia (qualifying round) APOEL (qualifying round; via Cypriot Cup) |
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← 1997-98
1999-00 →
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Statistics of Cypriot First Division in the 1998–99 season. The defending champion was Anorthosis. The league was performed with 14 teams, and Anorthosis won the championship.
| Pos | Team | Pld | Won | Drw | Lst | Pts | GF | GA | GD | Notes |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Anorthosis | 26 | 21 | 4 | 1 | 67 | 95 | 28 | +67 | UEFA Champions League 2nd Qualifying Round |
| 2 | AC Omonia | 26 | 21 | 4 | 1 | 67 | 81 | 25 | +56 | UEFA Cup Qualifying Round |
| 3 | APOEL | 26 | 19 | 2 | 5 | 59 | 70 | 29 | +41 | |
| 4 | AEK Larnaca | 26 | 14 | 3 | 9 | 45 | 63 | 45 | +18 | |
| 5 | AEL Limassol | 26 | 13 | 5 | 8 | 44 | 55 | 39 | +16 | |
| 6 | Ethnikos Achna FC | 26 | 12 | 6 | 8 | 42 | 49 | 43 | +6 | |
| 7 | Apollon Limassol | 26 | 13 | 2 | 11 | 41 | 51 | 45 | +6 | |
| 8 | Enosis Neon Paralimni FC | 26 | 8 | 8 | 10 | 32 | 55 | 64 | -9 | |
| 9 | Olympiakos Nicosia | 26 | 8 | 5 | 13 | 29 | 40 | 49 | -9 | |
| 10 | Nea Salamis FC | 26 | 8 | 4 | 14 | 28 | 46 | 53 | -7 | |
| 11 | Alki Larnaca FC | 26 | 7 | 4 | 15 | 25 | 37 | 70 | -33 | |
| 12 | Evagoras Paphos | 26 | 6 | 4 | 16 | 22 | 30 | 66 | -24 | Relegated to Second Division |
| 13 | Doxa Katokopia | 26 | 2 | 3 | 21 | 9 | 27 | 79 | -52 | |
| 14 | Aris | 26 | 3 | 0 | 23 | 9 | 32 | 96 | -64 |
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