Iraklis Thessalonikis traces its roots back on 1 July 1899 when Ómilos Filomoúson (Music Friends Club) was established.

The club was established as a cultural union of the Greeks of Thessaloniki (then under Ottoman sovereignty), and in 1902 was founded also a sport department.

Two years later, "Iraklís" (Heracles) was added to the club's name as an honour to the ancient Greek hero.

[3] Due to the revolt of 1908 of Young Turks and their promises for ease of ethnic tensions in the area, the club was forced to change its name.

[3] The new name was approved, together with a new statute and a new board of directors, by a general assembly of the club on 13 April 1911.