John Halls career began at Arsenal as a youth player. He played in the 2000 FA Youth Cup-winning team. He worked his way through the ranks and became a member of the first team but only made a few League Cup appearances. While he was still at Arsenal he was loaned out to Colchester United for 6 games and KSK Beveran for the whole of the 2002/03 season. He also spent 2 months at the beginning of the 2003/2004 season on loan to Stoke before he moved permanently for a small fee. Halls made 74 appearances at Stoke scoring 2 goals.