Stewart started his career with the Swindon Town he was a un-used substitute for the final game of the season, in his second year scholarship he was named as substitute in all fixtures under the management of Dennis Wise and later on Paul Storrock in league 2, upon the expiry of his contract moving to Weymouth in 2007 under then manager Jason Tindall, His Weymouth debut came on 18 September 2007 against Rushden & Diamonds in a 2–1 defeat; he was 18 at the time.
He spent one year at Weymouth Before leaving in 2008 to join then Premier league club Portsmouth under manager Harry Redknapp with whom he spent two seasons with, Stewart rejected the offer of a contract extension after his first season at the club deciding to sign for Spanish second tier team Alzira playing 10 games before returning to Portsmouth in November 2009, In 2010 Stewart signed for Bournemouth managed by Eddie Howe on a two-year deal as their second choice goalkeeper.
[4] On 11 February 2011 while at Bournemouth f.c, it was announced that Stewart will spend time training at Premier League club West Ham f.c under then goalkeeper coach David Coles with a view to a permanent transfer.
[13] In October 2014, Jon re-registered himself with Worksop Town and kept a clean sheet in the first appearance of his new spell in a 3–0 FA Vase victory away at Long Eaton United.
[15][16] In 2021 he joined Northern Premier League Division One East side Yorkshire Amateur for pre-season, but left before the opening game as the move did not work out.