| Pos | Team | P | W | D | L | F | A | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
Kelantan
| 26 | 18 | 6 | 2 | 53 | 18 | 35 | 60 |
| 2 |
Lions XII
| 26 | 15 | 5 | 6 | 48 | 23 | 25 | 50 |
| 3 |
Selangor
| 26 | 12 | 7 | 7 | 40 | 26 | 14 | 43 |
| 4 |
Perak
| 26 | 13 | 3 | 10 | 40 | 43 | -3 | 42 |
| 5 |
T'ganu
| 26 | 11 | 8 | 7 | 41 | 33 | 8 | 41 |
| 6 |
N9
| 26 | 10 | 7 | 9 | 41 | 38 | 3 | 37 |
| 7 |
PKNS
| 26 | 8 | 11 | 7 | 35 | 35 | 0 | 35 |
| 8 |
T-Team
| 26 | 10 | 5 | 11 | 35 | 36 | -1 | 35 |
| 9 |
Johor FC
| 26 | 10 | 5 | 11 | 29 | 31 | -2 | 35 |
| 10 |
Felda
| 26 | 11 | 2 | 13 | 25 | 31 | -9 | 35 |
| 11 |
Sarawak
| 26 | 8 | 6 | 12 | 28 | 32 | -4 | 30 |
| 12 |
Kedah
| 26 | 7 | 7 | 12 | 27 | 38 | -11 | 28 |
| 13 |
Sabah
| 26 | 7 | 7 | 12 | 33 | 52 | -19 | 28 |
| 14 |
KL
| 26 | 0 | 5 | 21 | 14 | 53 | -39 | 5 |
| Pos | Team | P | W | D | L | F | A | GD | Pts |
For Super League 2013: Competing team will be raduced from 14 to 12 teams.
11th~13th- Relegation Play Off with 2012 Premier League 2nd Place for 1 spot.
14th (Kuala Lumpur) - Will automatically relegated to 2013 Premier League
Premier League 1st Place: Will automatically promoted to 2013 Super League
