Iraklis traced its roots back in 1899 when "Omilos Filomouson" (meaning "Friends of Music Club") was established. The club was established as a cultural union of the Greeks of Thessaloniki, but in 1902 it founded a sports department. Football was a new sport at the time, but rapidly increasing in popularity and thus the board of directors decided to line up a football team. The first match that was held by the "Omilos Filomouson" football team was on 23 April 1905, against a team of the Western European diaspora of the city called "Union Sportive". "Omilos Filomouson" won the match by a 3–0 scoreline. Later on, the club faced financial problems, but members of the club joined forces with another Greek athletic club of the city, called "Olympia". The result of this union was the foundation of a new club on 29 November 1908, called "Makedonikos Gymnastikos Syllogos" (meaning "Macedonian Gymnastics Club"), that gained a permission to operate by the Ottoman authorities. The new club's first president was a Greek doctor, Alkiviadis Maltos. The name of the club had a direct reference to the ethnic tensions that took place in the area at that time. Due to the Young Turks' revolt of 1908 and their promises for ease of ethnic tensions in the area, the club was forced to change its name. Thus a new name was decided for the club, "Ottomanikos Ellinikos Gymnastikos Syllogos Thessalonikis "Iraklis"" (meaning "Ottoman Greek Gymnastics Club of Thessaloniki "Iraklis""). 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. After the integration of Thessaloniki in the Kingdom of Greece, the operation of the club was accepted by the Greek courts in 1914 and on 11 January 1915 Iraklis became a fully registered sports club.