Born in Crewe, Cheshire, Clayton started his football career at Crewe Alexandra Academy. Clayton made headlines in the media when the club's technical director Dario Gradi revealed a Premier League club had attempted to poach one of their 15-year-old players, which Clayton was named by the media. It was two years ago when Liverpool who had offered the Cheshire club a sum of around £1 million for the player's services two years ago. In March 2010, Clayton signed a long-term contract with the club.
Clayton made his debut for Crewe Alexandra in a 2–1 league win against Morecambe at the Alexandra Stadium on 22 April 2011, coming on as a second-half substitute for Shaun Miller. He made his second appearance of the season in a 2–0 away loss to Wycombe Wanderers, again coming on as a late substitute for Miller. Having made his debut for the club, Clayton signed his first professional contract with the club, which keep him until 2014.
He made his first appearance of the 2011–12 season on 6 August 2011, once again coming on as a late substitute for Miller as Crewe lost 3–0 away to Swindon. He began to get a regular run of games for Crewe, and scored his first goal in a 1–0 home win against Macclesfield Town in the JPT Trophy on 5 October 2011. His first league goal came in a 2–1 win on 19 November 2011 as he scored a 94th-minute winner against Morecambe, after England under-17 teammate Nick Powell had equalised for Crewe. He scored his second goal in a 2–0 home win against Accrington on 21 February 2012. On 10 March, he scored another 94th-minute winner as Crewe beat Gillingham 4–3.
On 16 May 2012, Clayton scored a vital goal in a 2–2 draw at Southened United to send Crewe to Wembley for the League 2 play-off final on a 3–2 aggregate score. Then in the 2012–13 season, Clayton scored twice in the first round of Football League Cup, in a 5–0 victory over Hartlepool United and then scored the only goal in the game, in a 1–0 win over Coventry City a few weeks later. His good display in August earned Football League young player of the month for August. Then on 7 April 2013, he scored in the 2013 Football League Trophy Final at Wembley Stadium, as Crewe beat Southend United 2–0. After the match, Clayton went on to say about the Football League Trophy as an unbelievable feeling.
After a prolonged absence due to a broken ankle sustained in November 2013, Clayton started negotiation for a new contract to stay at Crewe, which is believed to be a three-year contract. However, Clayton refused to sign a new contract at Crewe and left the club.
Clayton had trials at other clubs, including Wolverhampton Wanderers and Sunderland (he played in Sunderland's 5–1 pre-season victory over Darlington 1883 on 19 July 2014). Though Clayton left Crewe, it revealed that Crewe will receive six-figure compensation fee if Clayton was sold to a foreign club.
In early September 2014, it was reported that he was expected to join Bolton Wanderers. On 18 September 2014, he officially moved for a fee of £300,000 which had been set at a tribunal due to him being under the age of 24.
He made debut for the club on 4 October in a 2–1 home defeat to Bournemouth. After making four substitute appearances, he scored on his first start for the club in a 3–1 win at home to local rivals Wigan Athletic. After coming off injured in a 0–0 draw at home against Ipswich in December 2014, Clayton was ruled out for the rest of the season.
On 22 June 2017 it was confirmed that Clayton would join Blackpool on 1 July when his contract at Bolton expired.
He has also represented England at under-16, under-17 and under-18 levels, playing in the 2011 FIFA U-17 World Cup in Mexico. On 25 June 2011, he scored the second goal in a 2–0 victory over Uruguay in Torreón. He scored his first goal for the under-19 team on 24 May 2013 against Georgia.
His father Paul Clayton was a striker for Crewe Alexandra and his older brother Harry is currently a professional with Nantwich Town. Clayton grew up idolising Michael Owen.
Clayton says he is friends with Nick Powell, having played football together when they both five or six.As of match played 15 April 2017.
League Two play-offs (1): 2011–12
Football League Trophy (1): 2012–13