The 2003–04 Welsh Premier League was the 12th season of the Welsh Premier League since its establishment as the League of Wales in 1992. The league was won by Rhyl. Defending champions Barry Town F.C. were relegated after seven league championships and twelve seasons in the Premiership.
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Rhyl | 32 | 23 | 8 | 1 | 76 | 26 | +50 | 77 |
| 2 | Total Network Solutions | 32 | 24 | 4 | 4 | 77 | 28 | +49 | 76 |
| 3 | Haverfordwest County | 32 | 17 | 11 | 4 | 40 | 23 | +17 | 62 |
| 4 | Aberystwyth Town | 32 | 18 | 5 | 9 | 59 | 39 | +20 | 59 |
| 5 | Caersws | 32 | 15 | 10 | 7 | 63 | 41 | +22 | 55 |
| 6 | Bangor City | 32 | 16 | 6 | 10 | 72 | 47 | +25 | 54 |
| 7 | Cwmbran Town | 32 | 15 | 3 | 14 | 51 | 44 | +7 | 48 |
| 8 | Connah's Quay Nomads | 32 | 11 | 9 | 12 | 58 | 55 | +3 | 42 |
| 9 | Caernarfon Town | 32 | 11 | 9 | 12 | 65 | 65 | 0 | 42 |
| 10 | Newtown | 32 | 12 | 5 | 15 | 43 | 50 | -7 | 41 |
| 11 | Port Talbot Town | 32 | 11 | 6 | 15 | 41 | 51 | -10 | 39 |
| 12 | Porthmadog | 32 | 11 | 3 | 18 | 41 | 55 | -14 | 36 |
| 13 | NEWI Cefn Druids | 32 | 11 | 2 | 19 | 44 | 59 | -15 | 35 |
| 14 | Afan Lido | 32 | 8 | 8 | 16 | 31 | 54 | -23 | 32 |
| 15 | Welshpool Town | 32 | 6 | 7 | 19 | 25 | 71 | -46 | 25 |
| 16 | Carmarthen Town | 32 | 3 | 11 | 18 | 28 | 69 | -41 | 20 |
| 17 | Barry Town | 32 | 3 | 7 | 22 | 30 | 77 | -47 | 16 |
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