 Born in Skellefteå, Stefanidis started his career at youth level at IF Brommapojkarna and has also represented the Greek team Iraklis.He got his senior level debut for Djurgårdens IF in 2001, and won the Swedish Allsvenskan championship with the club in 2002 and 2003.In 2004, he moved abroad to play for Danish club Brøndby IF, with whom he won the 2005 Danish Superliga championship.