His only previous team is Olympique de Marseille, for whom he made twelve appearances between August 2003 and July 2004. He signed for Arsenal on July 23, 2004. He rejected a long-term senior contract with Marseille, after verbally agreeing to sign it, team coach Jose Anigo expressing, "This is a beautiful treason. He used me."

On January 13, 2005 the Court of Arbitration for Sport ruled that Flamini's transfer to Arsenal, which had been sanctioned by FIFA, was illegal. This decision could force Arsenal to pay Marseille further compensation for the player, having already paid around £300k, or even force Flamini to return to the French club. However, because the Court of Arbitration for Sport has no direct jurisdiction over English football, and FIFA sanctioned the transfer, it is highly unlikely that Arsenal will be forced to pay more compensation for the player or that Flamini will be forced to leave Arsenal.