Clarke began his career with Wolverhampton Wanderers but then played for twenty-three clubs – in both permanent and loan deals – over the subsequent years.

Having progressed through Wolverhampton Wanderers' youth academy, Clarke made his senior debut for his hometown club in a League Cup win over Darlington on 23 September 2003.

[4] After a loan period at Kidderminster Harriers in spring 2004,[5] he made his breakthrough into the Wolves first team in the 2004–05 season, making his league debut as a substitute in their opening match at Stoke City[6] and going on to score his first goal in the following game against Preston North End.

He angered sections of the Wolves' support after making a "shhh"-ing gesture toward the crowd after he scored a goal against Plymouth Argyle in January 2006.

[9][10] Although his manager, Glenn Hoddle, was not critical of Clarke's gesture,[9] the striker was only selected once more during the remainder of the season and was twice loaned out to other Championship sides; first to Queens Park Rangers,[11] then to Plymouth Argyle,[12] failing to score at either.

[16] The striker made five appearances for Oldham, netting three times; his first goal coming against League One rivals Doncaster Rovers in a 4–0 victory on 11 March 2007.

[18] The early stages of the 2007–08 season, saw him only start one game though and he was again loaned out, joining League One Southend United until January on the final day of the 2007 summer transfer window.

[40] After scoring six times in his first eight games, it was reported that Charlton were keen to use Clarke, once his loan spell ended and therefore Scunthorpe would be unable to sign him on a permanent basis.

[8][42] On Christmas Eve 2012, it was announced that Clarke had been given permission by Charlton to train with League One club Coventry City with a view to a permanent move.

[45] After a first start in a 0–3 defeat at Tottenham Hotspur in the FA Cup,[46] he signed a permanent two-and-a-half-year deal as a free transfer after Charlton had agreed to cancel his contract.

[47][48] Having scored his first goal for Coventry in a 3–2 victory over Preston North End in the Football League Trophy on 10 January 2013,[49] Clarke ended the 2012–13 season by scoring eight goals in eleven games in the league until an ankle complaint meant he underwent surgery in March, ruling him out for the remainder of the season.

[55] Amid this speculation Clarke entered a transfer request[56] and did not feature in a further match after citing a foot injury which provoked an unhappy reaction from his manager Steven Pressley.

[58] On 30 January 2014 Clarke rejoined his first club Wolverhampton Wanderers, now playing in League One, after signing an eighteen-month deal (with Wolves holding the option of an additional year) for an undisclosed fee reported to be £750,000.

[61] He made his second Wolves debut on 1 February in a 2–0 win over Bradford City,[62] with his first goal since rejoining coming on 11 March in a 4–1 victory at Swindon Town.

[64] Back at Championship level, Clarke scored twice during 16 league appearances before being loaned out in February 2015 to Wigan Athletic for the remainder of the season.

[68] On 11 August, he continued his good form by scoring a brace in a 2–1 win over former team Wigan Athletic in the first round of the League Cup, including the go ahead penalty in the 89th minute.

[79] Clarke made his first ever appearance in the Premier League on 28 September 2019, coming on as a substitute in a 1–0 loss against Liverpool,[80] at the age of 34, and 16 years into his professional career.

[84] On 17 October, Clarke scored his first goal for the club, heading in a 91st-minute winner from a Josh Vela corner away to AFC Wimbledon at the Kiyan Prince Foundation Stadium.

[87] Clarke made his debut for the club that weekend, coming on as a half-time substitute and within 90 seconds he had scored with his first touch of the ball, the only goal in a victory over Crawley Town.

[98] On 29 September 2023, it was announced that Clarke had signed for Southern League Premier Division Central club Kettering Town.