Cowley was born in Havering, London. He was involved with the youth set-up with Wimbledon from the under-10s to under-16s but was not offered a scholarship having suffered from Osgood–Schlatter disease.
When he took over at Concord Rangers, the club was playing in the Essex Senior Football League, in front of crowds of around 50 people. In his first season the club was promoted to the Isthmian League Division One North, and narrowly missed out on a second successive promotion the following year, before being promoted a year later. After two seasons of consolidation, Cowley won his third promotion with the club, this time to the National League South. In his last season in charge, Concord reached the first round proper of the FA Cup, while narrowly missing out on a play-off spot.
On 30 April 2015, Cowley became manager of Braintree Town. That season Braintree secured their highest-ever finish of third place in the National League, and qualified for the play-offs. In the play-off semi-finals, they won the first leg at Grimsby Town, defeating them 1–0, before losing the second leg 2–0 at home, failing to qualify for the final as his side lost 2–1 on aggregate.
After just one season in charge of Braintree Town, Cowley moved on again, this time to Lincoln City on 13 May 2016. During Cowley's first season in charge of Lincoln, he oversaw the club's promotion back to the Football League - doing so by winning the National League title with two games to spare. This, after a six-year absence since relegation in 2011. In the same season Lincoln became the first non-league club to reach the quarter-final of the FA Cup in over a century, knocking out Championship sides Ipswich Town and Brighton & Hove Albion, followed by Premier League side Burnley, in the process. Lincoln eventually lost 5–0 to Arsenal in the quarter-finals. In April 2018, with their contracts due to end in 2021, Cowley and his brother signed contract extensions lasting until 2022. On 8 April 2018, he led his team to the EFL Trophy final against Shrewsbury Town at Wembley Stadium which they won 1-0 owing to a goal by Elliott Whitehouse. It was Lincoln's first ever game at Wembley. In Lincoln's first season back in the league they finished the season seventh in League Two. The following season, Cowley guided Lincoln to promotion to League One, returning to the third tier of English football for the first time since 1999. On 22 April 2019, Cowley led Lincoln as champions to League One after a 0–0 draw at home to Tranmere Rovers.
Huddersfield Town
On 9 September 2019, Cowley left Lincoln to become the new Huddersfield Town manager. He and his assistant Nicky signed 3-year contracts. After a successful run of 6 games unbeaten throughout the month, Cowley won the EFL Championship Manager of the Month award for October 2019. Despite defeating promotion seeking West Brom 2–1 to ensure that the club would remain in the Championship, Cowley was sacked two days later on 19 July 2020. Chairman Phil Hodgkinson outlined the need for a "different vision" going forward as the reason for relieving Cowley of the role.
Personal life
Growing up, Cowley was a West Ham United supporter. During his spells as manager of Concord Rangers and Braintree Town, Cowley combined his management role with teaching Physical Education at FitzWimarc School in Rayleigh, Essex. Cowley has a brother, Nicky, who played alongside him at Romford and has been his assistant manager at Concord Rangers, Braintree Town, Lincoln City and Huddersfield Town. Cowley graduated from the University of Greenwich in 2002, obtaining a bachelor's degree in Physical Education.
