The men's team played in Sweden's highest division, SSL, from the year 2000, but was relegated to Herrar Allsvenskan Norra in 2018 after ending the season 2017/2018 as second last.

The inaugural season in the Svenska Superligan saw AIK set new attendance records for league matches.

In a match against the then reigning Swedish champions, Haninge IBK, a total of 3,000 spectators attended, setting a new record (at the time).

The following season (2003–04) saw AIK Innebandy go all the way to the final, only to lose to rivals Balrog IK 6:5 in the championship match.

They then repeated the feat in 2007–08, beating Warberg IC once again, 2:1 in overtime, in a rematch of both the 2006–07 EuroFloorball Cup and the 2007–08 Svenska Superligan final.

The 2008 EuroFloorball Cup saw AIK win once again; this time against Swiss team SV Wiler Ersigen.