Clarke-Harris was playing park football in Leicester for Beaumont Town and Judgemeadow under 16s when Mick Elliott MBE, then Coventry Head of Recruitment, brought him to the club for a trial. With his strong physique and pace, he made an immediate impact playing a trial game for Judgemeadow against a good Coventry City U16 team and he was given a scholarship offer by Coventry City Academy. Clarke-Harris made his professional debut as a substitute on 10 August 2010 in a 2–0 League Cup loss to Morecambe, coming on to replace David Bell after 68 minutes. With this appearance he became the youngest player to ever appear for Coventry City. He was 16 years and 20 days old. It was confirmed on 30 April 2012 that Clarke-Harris had not been offered a professional contract with Coventry and had left the club. Andy Thorn refused to speculate on why Clarke-Harris had been released but alluded to disciplinary problems.
On 8 May 2012, he played in a reserve match for Blackburn Rovers, scoring the only goal of the game. On 23 July he signed a two-year contract with Peterborough United. Without having made a first team appearance for Peterborough United and was loaned out on 12 October to Southend United for a month.
Clarke-Harris signed for Oldham Athletic from Peterborough United for an undisclosed fee, agreeing a one-year contract with the club and an option for a further year in the clubs favour in May 2013 . His first goal for the club was a 25-yard free-kick in a 3–2 defeat to Notts County. On 7 February 2014, Clarke-Harris was rewarded for his continued improvement with an eighteen-month contract extension.
Clarke-Harris ended his first season with the club with 8 goals in 49 appearances in all competitions. After many excellent performances throughout his first season, he won the Young Player of the Season award at the end of season awards. Upon receiving the award, Clarke-Harris thanked the fans and everyone at the clubs for support of his progression during his first season with the club, and he vowed to work even harder and to "continue scoring goals for Oldham Athletic".
On 1 September 2014, Rotherham United announced that they had signed Clarke-Harris for a club record fee, rumored to be in the region of £350,000. He scored his first goal for Rotherham with a 25-yard strike that gave them the lead in a 2–1 win over Leeds United. Clarke-Harris then made it 2 in 2 games just a few days later, scoring Rotherham's second goal in a 3–3 draw with Fulham. Inconsistent form within the Rotherham side that season led to him leaving the club on two different loan spells to get some game time. He finished the 2014–15 season for Rotherham with 3 goals in 15 appearances.
In the 2015–16 season, Clarke-Harris failed to make the matchday squad for the first three games of the season. Consequently, manager Steve Evans sanctioned a potential loan move to Colchester United, and in hindsight said that Clarke-Harris' Rotherham career was nearly over. However, he made his first appearance of the season in a 0–0 draw with Preston North End, coming on as a substitute. His impressive performance led to him starting the following game against Queens Park Rangers, where he scored Rotherham's first goal in a 4–2 defeat. He also started the next league game against Fulham, scoring Rotherham's only goal in a 3–1 defeat.
Clarke-Harris missed the majority of the 2016–17 season after suffering a cruciate ligament injury in his first pre-season friendly, however he returned to the team to finish the season strongly and signed a new one year contract with the club on 9 May 2017.
On 16 January 2015, Clarke-Harris signed on loan for Milton Keynes Dons on a short one-month deal until 21 February 2015. He made five appearances scoring no goals before returning to Rotherham for the remainder of the season.
On 12 March 2015, Clarke-Harris completed a loan move to Doncaster. He made 8 appearances scoring one goal against his old club Coventry City.As of match played 7 May 2017