He scored the winning goal for Ipswich Town against Southampton in the FA Youth Cup final in 2005 when he was 15, and signed a professional contract at the age of 17. In 2008, he was loaned to Stevenage Borough, where he made one substitute appearance on 2 September against Kettering Town. He made his Ipswich debut as a substitute in a Football League Cup match at Shrewsbury Town on 11 August 2009. The match went to penalties after a 3–3 draw and Upson scored one of the penalties to help Ipswich through to the next round. After being scouted on many occasions by Barnet manager Ian Hendon, Upson joined the Bees on loan from 12 March 2010 for one month, and made his debut coming on as a second half sub for Albert Jarrett in the 1–1 home draw with Burton Albion. Upson was released by Ipswich at the end of the 2009–10 season.
He joined Yeovil Town on a two-year contract at the start of the 2010–11 season. He scored his first goal for Yeovil in the FA Cup match with Hartlepool United in 2010. On 13 August 2011, he scored his first league goal from outside the area in a 3–1 win over Oldham Athletic, and went one better with a strike from 30 yards to seal a 1–0 win against Wycombe Wanderers on 13 September 2011, this goal was later nominated for Mitre Goal of the Year. He also scored twice in the FA Cup, with goals in the 3–0 win over Hereford United, and the 2–2 draw with Fleetwood Town. On 6 May 2013, Upson scored an 85th-minute goal in the 2013 Football League play-offs, to help Yeovil beat Sheffield United 2–1 on aggregate, to taking Yeovil to Wembley for the playoff final. A play-off final which they won 2–1 earning promotion to the Football League Championshipfor the first time in the club's history. On 3 August 2013, Upson scored the winning goal as Yeovil won their first ever game in the Championship, to secure a 1–0 victory at Millwall.
Millwall
On 31 January 2014, Upson signed for Championship club, Millwall, for an undisclosed fee signing a two-and-a-half-year contract.
On 3 June 2016, Milton Keynes Dons announced that Upson had signed a two-year deal with the club and would join the squad on 1 July 2016 following his release from fellow League One club Millwall. On 16 August 2016, Upson scored his first goal for the club, scoring in the 94th minute in a 1–2 home defeat to Bradford City. On 26 November 2016, Upson scored twice in a 1–2 away win over Coventry City.
Bristol Rovers
On 22 May 2018, it was announced that Upson would leave recently relegated MK Dons and join Bristol Rovers effective from 1 July 2018 upon his contract ending at Milton Keynes.
