A defender, primarily at right-back but sometimes in the centre or in midfield, he began his career with Tottenham Hotspur, winning the FA Youth Cup in 1990. He made his first-team debut in 1989, and made seven appearances for the club over the next four years, also representing England Under-21 seven times.
Joining up with his mentor Peter Shreeves, who has coached him at Tottenham and Sheffield Wednesday, he captained the club in their return to the Football League in his second season, and remained a key player for four years. At the end of the 2006–07 season, Hendon faced a dilemma. Initially, he was not offered a new playing contract by Barnet, but was given the chance to join Paul Fairclough's coaching staff. Nevertheless, he featured in the early fixtures of 2007–08, before dropping back as new players arrived. He remained registered as a player until the end of the 2008/09 season when he retired as a player to concentrate solely on management.
Following Paul Fairclough's step-down after the 3–0 Boxing Day defeat to Aldershot Town, Hendon was asked to take over the side. Fairclough's last game was a 2–0 win at A.F.C Bournemouth, leaving the side with 19 points from their 23 league games. Performances improved under Hendon, and some adept loan signings including Paul Furlong, Matt Lockwood, Jake Cole and Yannick Bolasie helped to drag The Bees away from the relegation battle and to mathematical safety with four games to spare.
He declared his desire to take the job permanently[dead link] and was given the job on a 2-year deal in April 2009. The Bees started the 2009/10 season in superb form and were top of the league at one point, but Hendon was sacked on 28 April 2010 after a disastrous run of form left the Bees in serious relegation trouble. The last game of Hendon's reign was a 1–0 defeat to Accrington Stanley. On 28 May 2010, he was appointed the manager of Conference South side Dover Athletic, but just 18 days later quit the club to become assistant manager to his former Bees team-mate Andy Hessenthaler at Gillingham. Hessenthaler had been his predecessor as Dover manager. In July 2011 he was appointed, by new manager Sam Allardyce, as development coach at West Ham United. In December 2012, he was promoted to the role of first-team coach following the departure of Wally Downes.
On 28 May 2015, it was announced Hendon would be returning to Brisbane Road as Leyton Orient's new manager, replacing Fabio Liverani following the club's relegation to League Two