Born in Marseille, Flamini was a youth team player for his local professional club Marseille. He made his debut for the senior team on 20 December 2003 in the 1–0 victory over Toulouse. He impressed the team as a hardworking midfield player and played 14 times for the club. However, it was his performances in Marseille’s UEFA Cup campaign that brought him to the attention of the football world, including the 2–0 semi-final victory over Newcastle United. He then started in the Final in Gothenburg, a match Spanish club Valencia won 2–0. Due to his age, however, Marseille was later unable to offer him a long-term professional contract.