Stelios Giannakopoulos began his professional career in 1992, playing with Ethnikos Asteras.

In 1993 he moved to Paniliakos, where he stayed for 3 years. In the summer of 1996, he signed with Olympiacos and, during the next seven seasons, he had a total of 189 appearances, scoring 63 goals. He won the Championship with Olympiacos for 7 consecutive years and reached the Champions League quarter-finals in 1998-1999.
In 2003 he was acquired by Bolton, where he stayed until 2008.

On September 2008, he signed with the Premiership club Hull City, and in 2009 he returned to Greece, to play for AEL, where he finished his career one year later.

His debut with the Greek national team took place on March 12, 1997.

In Euro 2004, he was one of the key players of the team’s impressive run, which ended with the conquest of the trophy.

In May 2010, he came first in the PSAP elections, succeeding Antonis Nikopolidis in the presidency of the Association.