This is the 2008-09 Atlantic Junior Hockey League season. This is the league's sixth season overall.
All 11 franchises returned from the previous season and the league adds the Philadelphia Jr. Flyers.
Standings[]
| North | GP | W | L | OTL | PTS | GF | GA |
| Northern Cyclones | 42 | 35 | 6 | 1 | 71 | 206 | 82 |
| Hartford Jr Wolfpack | 42 | 27 | 10 | 5 | 59 | 143 | 98 |
| Walpole Express | 42 | 25 | 12 | 5 | 55 | 136 | 191 |
| Boston Jr. Bulldogs | 42 | 20 | 17 | 5 | 45 | 136 | 122 |
| Portland Jr. Pirates | 42 | 13 | 27 | 2 | 28 | 98 | 180 |
| Laconia Leafs | 42 | 5 | 36 | 1 | 11 | 66 | 204 |
| South | |||||||
| New York Bobcats | 42 | 34 | 7 | 1 | 69 | 175 | 106 |
| New Jersey Rockets | 42 | 27 | 14 | 1 | 55 | 182 | 125 |
| Philadelphia Little Flyers | 42 | 20 | 20 | 2 | 29 | 137 | 154 |
| Philadelphia Jr. Flyers | 42 | 19 | 20 | 3 | 41 | 124 | 148 |
| Washington Jr. Nationals | 42 | 17 | 19 | 6 | 40 | 135 | 145 |
|
Binghamton Jr Senators |
42 | 10 | 28 | 4 | 24 | 87 | 170 |
Playoffs[]
Playoffs were won by the Northern Cyclones