Henderson is from Craigavon, County Armagh.[1] He grew up in Lurgan and played snooker as a child, going on to represent Northern Ireland as a junior international in 2003.[2] He was on the books at Portadown as a youth player, before moving to Scotland with Gretna at the age of 16.[3] He first featured on the bench for Gretna in their 2–1 defeat to Stirling Albion on 29 April 2006 in the Scottish Football League Second Division,[4] and was subsequently on the bench for the 2006 Scottish Cup Final against Heart of Midlothian, which was lost 4–2 on penalties after a 1–1 draw after extra time on 13 May 2006.[5] He was loaned out to Dumbarton in the Scottish Third Division in August 2007 until January 2008,[6] during which he made 16 appearances and scored one goal.[7] He was released by Gretna in January and signed for Raith Rovers later that month on a short-term deal to the end of the 2007–08 season,[8] making his debut in the 1–0 victory at Queens Park on 19 January 2008 at Hampden Park.[9] Henderson featured for the side in both legs of their play-off semi-final defeat to Airdrie United and finished the season with 16 Raith appearances.[10][11][12]
He was released by Raith after the end of the season,[13] after which he joined York City in the Conference Premier on 18 June 2008.[14] He made his debut in a 1–0 victory against Wrexham on 14 August 2008 after coming on as a 62nd-minute substitute.[15] He was named in the Northern Ireland under-21 team in September for their 2009 UEFA European Under-21 Football Championshipqualifying game against Germany.[16] Henderson was on the bench as Northern Ireland were beaten 3–0,[17] meaning they were unable to quality for the tournament.[18] He made his return for York in a 4–2 defeat to Kettering Town, which was the team's first loss of the season.[19] He suffered from two viruses within the space of four weeks, and returned to light training in October.[20] He continued to play for the reserve team and scored in a 4–4 draw against Barnsley reserves.[21][22] Henderson had fallen out favour under manager Colin Walker and struggled to feature in the team.[23] He picked up a hamstring injury during a training session in December.[24] He was released by the club on 20 January and returned to Ireland to sign for either Finn Harps or Newry City,[25] eventually signing for Newry.[26]
On 6 July 2010, Henderson joined Dungannon Swifts on a one-year deal along with Johnny Topley after his contract with his previous employers, Newry City, expired. In June 2011 he joined Glenavon.