At the start of the 2000/2001 season Emanuel Pogatetz moved on a free-transfer from
SK Sturm Graz
to FC Kaernten, who were at this time playing in the Austrian Erste Liga (second highest division in Austria).
The Head-Coach of FC Kaernten, Walter Schachner thought the world of Emanuel Pogatetz and supported, developed and encouraged him as much as possible.
Only in his first Season in professional football he was already a regular in the first team of his club.
He played a vital part in FC Kaernten sensationally winning the Austrian Cup for the first time in the history of the football club, winning the Championship in their Division and also gaining promotion to the Austrian Bundesliga.
Emanuel Pogatetz also earned himself a spot in the Austrian Under 21 National Team whilst playing for FC Kaernten.