In 2003 Armagh once again reached the All-Ireland final, but were defeated by neighbours Tyrone. 2004 saw Clarke and Armagh again win the Ulster Championship.
In 2005 Clarke helped Armagh win the National League, beating Wexford in the final. Later that year he helped Armagh win another Ulster Championship.
Clarke helped Armagh win the 2006 Ulster Championship and was named Irish News Ulster All-Stars Player of the Year. It was the second time he had been selected on the Ulster All-Stars team. He was awarded an All Star award for his 2006 performances with Armagh. He was also named in the 2006 GPA Team of the Year and nominated for GPA Footballer of the Year.
Clarke missed the 2007 season due to a cruciate ligament injury suffered in the 2006 season. He won another Ulster Championship medal with Armagh in 2008 and was awarded another All Star for his performances throughout that year's Championship.
Clarke helped Pearse Óg win the 2000 Ulster Minor Club Football Championship, which he described as his greatest moment in sport. Clarke has reached the Armagh Senior Football Championship final with Pearse Óg on a number of occasions, but they have been defeated by Crossmaglen each time until 2009, when Clarke helped Pearse Óg defeat Crossmaglen in the quarter final of the Armagh Senior Football Championship ending Crossmaglens 13 year win streak in the competition. Pearse Óg went on to win the Championship defeating city rivals Armagh Harps on a scoreline of 0-8 to 0-4 earning Clarke his first Senior County medal.