Emanuel Pogatetz started his career at the age of 7 at his hometown club SK Sturm Graz, after he also tried to play ice-hockey. He passed through all the teams at every age group, where especially his coaches Dietmar Windisch and Alfred Werner had a huge impact on his future career.
Emanuel Pogatetz was able to win a few trophies whilst playing for the SK Sturm Graz Youth-Teams :
- Styrian Under 10 Championship
- Styrian Under 12 Championship
He also participated in several Youth Selections whilst playing for the SK Sturm Graz Youth-Teams :
- ASVÖSelection Styria
- Austrian National TeamUnder 16: 22 Games
- Austrian National Team Under 18: 05 Games
- Austrian National Team Under 19: 03 Games
At the age of 16 he made it in to the squad of the first team of SK Sturm Graz, who were at this moment playing in the Champions League and also recently won the Austrian Double (Champions of the Austrian Bundesliga -highest football division in Austria - and winners of the Austrian Cup). There he was able to benefit from training on first-team level but also from training under Ivica Osim, who was the head-coach of SK Sturm Graz back then.
On 04.04.2000 he was for the first time part of the first-team squad of SK Sturm Graz for the Austrian Cup game away at ASKOE Pasching. Unfortunately the game was lost 5:4 after penalties.
At this time German Bundesliga Giants FC Schalke 04 wanted to sign Emanuel Pogatetz for their team, but he decided that it was too early for him to go abroad and so he rejected the offer and decided to stay in Austria a little bit longer.