History
The club was established in 1994 after a merger of Arisvaios Kalloni (est. 1954) and Apollon Dafia (est. 1969), two clubs that had been based in villages in the wider area of Kalloni, the club's original seat.
2002–03 season
In 2002 they promoted in Delta Ethniki but they relegated to local championship of Lesbos. Being one of the weakest club of their group and without having any professional contract, they only achieved four wins.
2007–08 season
The advent of Prokopis Kartalis who had played at Alpha Ethniki as a player of Skoda Xanthi marks the beginning of the glorious course of the club. Kartalis emerged team's top scorer and AEL Kalloni easily won Lesbos local championship and the promotion to Delta Ethniki.
2008–09 season
In 2008–09 season, they promoted in Delta Ethniki and, even though outsider, they came close to take the first place. They were placed in a group that also competed Athenian clubs and finished 5th.
2009–10 season
During the 2009–2010 season AEL Kalloni, making an amazing second round and having the best defense and the second best goals for record in their group won the first place and, for the first time ever, promotion to Football League 2.
2010–11 season
In the club's first season in a professional league, in the North Group of Football League 2, they placed 2nd, a place that led them to a mini league (play-offs) against Vyzas, the 2nd-place team of South Group, and the third-placed teams of each group, Fokikos and Iraklis Psachna. The winner of the league would be promoted in Football League. However, due to the relegation of five clubs by the previous version Football League, play-offs were not carried out, so Kalloni promoted directly with all clubs that would have competed in play-offs, Anagennisi Giannitsa and Platanias to 2011–12 Football League.
Kalloni seasons
| Season | Division | Tier | Position |
|---|
| 1994–95 | Lesbos FCA Championship | V | 4th |
| 1995–96 | Lesbos FCA Championship | 1st ↑ |
| 1996–97 | Delta Ethniki | IV | 13th ↓ |
| 1997–98 | Lesbos FCA Championship | V | 2nd |
| 1998–99 | Lesbos FCA Championship | 2nd |
| 1999–2000 | Lesbos FCA Championship | 1st |
| 2000–01 | Lesbos FCA Championship | 4th |
| 2001–02 | Lesbos FCA Championship | 1st ↑ |
| 2002–03 | Delta Ethniki | IV | 15th ↓ |
| 2003–04 | Lesbos FCA Championship | V | 4th |
| 2004–05 | Lesbos FCA Championship | 5th |
| 2005–06 | Lesbos FCA Championship | 2nd |
| 2006–07 | Lesbos FCA Championship | 2nd |
| 2007–08 | Lesbos FCA Championship | 1st ↑ |
| 2008–09 | Delta Ethniki | IV | 5th |
| 2009–10 | Delta Ethniki | 1st ↑ |
| 2010–11 | Football League 2 | III | 2nd ↑ |
| 2011–12 | Football League | II | 5th |
| 2012–13 | Football League | 3rd ↑ |
| 2013–14 | Super League Greece | I | 12th |
| 2014–15 | Super League Greece | 10th |
| 2015–16 | Super League Greece | 16th ↓ |
| 2016–17 | Football League | II | 16th ↓ |
- Delta Ethniki was abolished in 2013, as it was merged with Football League 2, the third tier of the Greek football league system.
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