Clarke is a goalkeeper and played schoolboy football for local side Cherry Orchard. He is one of a handful of local players to have played for St. Pats. Clarke had an extended spell in the first team at the end of the 2004 season as regular 'keeper Chris Adamson's form dropped. In 2007, Clarke was sent on a season-long loan to Waterford United but was recalled before the season got underway. At the end of the 2007 season, Clarke played in the 4 of the last 5 league games. Keeping 3 clean sheets out of 4 ensuring the Saints secured UEFA Cup football in 2008. He only missed the last game of the season due to an injury during the warm-up. He had a very successful loan spell at Sporting Fingal F.C. during the 2nd half of the 2008 season. He played 14 games for Fingal, keeping 7 clean sheets. When coming back to the Saints for the 2009 season, Clarke was told by the then boss, John McDonnell, that he'd be his number 1 goalkeeper for the season. McDonnell then left the club and was replaced by Jeff Kenna as manager. Kenna let goalkeeper Barry Ryango toGalway United and replaced him with Galway keeper Gary Rogers. Kenna favoured Rogers from day one and installed Rogers as his number 1 keeper. When Jeff Kenna resigned, new manager Pete Mahon came in and immediately put Clarke into the team. Clarke played in the final 10 games of the 2009 season and put in some fine performances. He kept 4 clean sheets in the 10 games including clean sheets against the Saints relegation rivals Bray Wanderers twice and Dundalk, and also keeping a clean sheet in the vital last game of the season against Shamrock Rovers.
Sporting Fingal
Following the 2009 season, Clarke signed a 2-year full-time contract with Sporting Fingal, where he'd had a very successful loan spell in 2008.
After Sporting Fingal ceased trading Clarke's contract was cancelled and he signed for Sligo Rovers on a 1-year full-time contract on 15 February 2011. Clarke impressed immediately by saving a penalty on his debut in the 1–0 win over Derry City F.C. in The Brandywell. He followed this up by keeping 5 clean sheets in his first 6 games. He has gone on a great run and has currently kept 9 consecutive clean sheets, setting a new League of Ireland record for consecutive clean sheets. This has helped Rovers move to the top of the Airtricity LeaguePremier Division. Solid performances from Clarke helped Sligo to a 2nd-place finish in the league and also a cup winners medal as Sligo lifted the FAI Cup for the second year in a row.
Return to St. Patrick's Athletic
Clarke signed a contract to return to the Saints for the 2012 season on 21 December 2011. He earned his place as number one keeper ahead of Barry Murphy and kept five clean sheets in the opening eight games of the season, conceding only three goals. Clarke remained at the Saints for five seasons, in which he won the League in 2013, the 2014 President's Cup, the 2014 Leinster Senior Cup, the 2014 FAI Cup, as well as the League Cup in 2015 and 2016.
He has represented the Republic of Ireland at schools international level and was selected as part of the Republic of Ireland Under 23 squad to play Northern Ireland in 2008.