Sheffield Hallam Eagles On 24 February 2013, Henderson was appointed the head coach of a new community club, Sheffield Hallam Eagles, run by
Sheffield Eagles, and Sheffield Hallam University. In their first season, Henderson's team lost just once all season, winning the
Conference League South beating
Nottingham Outlaws in the grand final.
London Broncos On 11 July 2014,
London Broncos head coach
Joe Grima appointed Henderson as his assistant beginning in November. On 2 March 2015, Joey Grima resigned after ten months in charge and just three games into the Championship season. Henderson took charge of the Championship side on an interim basis. After 2 games in charge with 1 win and 1 loss, he was appointed as the Broncos new permanent head coach. In 2015, Henderson led the Broncos to 3rd place in the
Championship Shield, eventually losing the Shield Final to
Featherstone Rovers 34–6 at the
Select Security Stadium in Widnes. In 2016, he guided the London Broncos to a 2nd-place finish in the Championship taking them into the Super 8's Qualifiers for the chance to gain promotion. The club finished a reasonable 6th place on points difference with wins over Batley, Salford and Featherstone. They just missed out on the million pound game to Salford. In 2017, they again finished 2nd in the Championship and 6th place in the Super 8's Qualifiers. Henderson was awarded the Kingstone Press Championship Coach of the Year award after another successful season with London. The London Broncos won on all three occasions under the guidance of Henderson at the
Summer Bash event. They recorded a 42–6 win and 32–14 win over the Sheffield Eagles in 2015 and 2016. In 2017 they defeated Featherstone Rovers 42–16.
Warrington Wolves Henderson joined Warrington ahead of the 2018 season as assistant coach to Steve Price. He spent 4 seasons at the club before moving into a Head of Rugby role with the Keighley Cougars. During his time the team finished as Challenge Cup and grand finalists in 2018, followed by a Challenge Cup final win in 2019. His final two seasons saw the wolves finish as semi finalists in both competitions.
York Knights On 18 October 2022, Henderson signed a five-year deal to become the new head coach of
York Knights. On 5 June 2024, it was reported Henderson had taken the position of Head of Rugby at York and that the head coach role had been handed over to
Mark Applegarth. ==Coaching statistics==