Thomson began his career at
Southampton in 2005 and was promoted to the first team in 2008, making his debut on 9 August 2008 against
Cardiff City in the
Football League Championship. He made a further nine appearances for Southampton in the 2008–09 season. Thomson spent one month on loan to
Bournemouth between January and February 2009; although the clubs had agreed to extend the loan, this was not permitted because of Bournemouth's financial circumstances. Thomson made four appearances for Southampton in the
2009–10 Football League One. On 27 October 2009, he joined
Torquay United on loan for a month. The loan was extended until the end of the 2009–10 season. He was released by
Southampton on 15 May 2010. On 1 July 2010, he was signed by
Exeter City. On 25 February 2011, Jake signed on loan to
Cheltenham for an initial one-month loan. He was one of twelve players released by Exeter in May 2011. Thomson spent the summer of 2011 on trial with
Southend United however he failed to earn a deal. Thomson subsequently signed for
Conference National outfit
Kettering Town. Shortly after joining Kettering however on 27 September 2011, Thomson joined fellow Conference National side
Forest Green Rovers on loan. He made his Forest Green debut on the day he signed, coming on as a second-half substitute in a 1–1 draw with
Newport County at
The New Lawn. In October 2011, Thomson had his loan deal extended at Forest Green by a further month. In November 2011 it was announced that Thomson's loan spell at Forest Green would be turned into a permanent move. After making 28 league appearances for Forest Green, Thomson was released by the club in May 2012. He signed for Newport County on 11 June 2012. In January 2013 Thomson joined
Lincoln City on a one-month loan and he returned to Newport County in February 2013. In the 2012–13 season he was part of the Newport team that finished 3rd in the league, reaching the Conference National playoffs. Newport County won the playoff final versus Wrexham at Wembley stadium 2–0 to return to the Football League after a 25-year absence with promotion to League Two. After a break from football, Thomson joined
Horndean in August 2020. The following season he was playing for
AFC Stoneham. Thomson joined
Brockenhurst in July 2022. In November 2022, he rejoined AFC Stoneham as a player/coach. In his first appearance back at the club, he scored a hat-trick against the side he had just left, Brockenhurst. In December 2023, he joined
Petersfield Town. ==International career==