Cooper was first called up to the Kerry Senior team in 2002. After strong performances in the National Football League, he continued his rise in that year's Championship, with excellent performances against Wicklow, Kildare, Galway and Cork on route to the All-Ireland final, where they faced Armagh. Armagh defeated Kerry in a close encounter. Cooper was awarded an All Star award for his performances that year.
In 2003 Kerry won the Munster Senior Football Championship, but were knocked out of the All-Ireland Championship by Tyrone at the semi-final.
2004 proved to be a very successful year for Cooper and Kerry. It began with the county winning the 2004 National League, with victory over Galway in the decider. They also defended their Munster title, before going on to win the All-Ireland Championship – beating Mayo in the final. Cooper put in another excellent performance in the final, scoring 1–05 including a superb individual goal where he fielded a high ball under pressure before taking on three defenders and slotting it into the Mayo net. He received another All Star and was named Texaco Footballer of the Year.
Kerry won their third consecutive Munster Championship in 2005, beating old rivals Cork in the decider. Kerry once again reached the All-Ireland final, this time against Tyrone. After a bright start, Cooper was injured in a clash with Tyrone goalkeeper Pascal McConnell which limited his involvement. Tyrone won the game 1–16 to 2–10. He did however win a third All Star.
Cooper won a second National League medal with Kerry in 2006, once again beating Galway in the final. In the Championship Cork defeated Kerry in the Munster final. Kerry however, did advance to the All-Ireland final, where they once again met Mayo. Kerry won the game by 13 points and Cooper was again one of Kerry's main contributors scoring 1–02. He was the Kerry captain for part of that year, although regular captain Declan O'Sullivan was restored as captain for the All-Ireland final. After winning the game, the Sam Maguire Cup was lifted by both O' Sullivan and Cooper. He was nominated but not selected for an All Star that year.
In 2007 Cooper was instrumental in Kerry regaining their Munster Championship title after an enthralling game against Cork, which Kerry won 1–15 to 1–13. Having been quiet for long spells, he burst into life and in a five minute period scored 1–02. After beating Dublin by two points in the semi-final, Kerry progressed to face their bitter rivals Cork in the first ever all-Munster All-Ireland final. Kerry comfortably beat Cork 3–13 to 1–09, to become the first team to retain the title since Cork themselves 17 years before. Cooper got the goal that put Kerry in the driving seat, rising to fist the ball over the onrushing Alan Quirke. Cooper finished the game with 1-05. He received another All Star and was nominated as one of three contenders for 2007 Footballer of the Year. He was also named on the GPA Team of the Year.
Kerry reached the 2008 National League final, but were beaten by Derry. Cork beat Kerry in the 2008 Munster final. Kerry nevertheless advanced to the All-Ireland final, to face Tyrone for the third time in six years. Tyrone once again came out on top. Cooper did however win a fifth All Star award that year and was once again named on the GPA Team of the Year.
Colm Cooper made a poor start to the 2009 championship in the Munster championship and early qualifier games by his own standards. He and Tomás Ó Sé were dropped from the starting Kerry 15 for the qualifier game against Antrim, due to a breach of team discipline. Cooper came on against Antrim and made an immediate impact notching 4 frees in another win for Kerry. Kerry progressed to face Dublin in the quarter final and were given little chance of beating a Dublin side after winning their fifth Leinster Championships in a row. Dublin had the usual support of a strong Croke Park crowd and media behind them. However, within a minute Cooper had Kerry in front with a goal. They nullified Dublin's tradition of making a strong start by making a blitzkrieg of their own and were a whopping 1–13 to 0–03 ahead at the break. The game ended with Kerry on top by a 17-point margin and Cooper announcing his return to form with a haul of 1–08. Cooper and Kerry brushed Meath aside in a low-key semi final before they faced against Cork in the semi final. For the first time in their six meetings in Croke Park, the rebels were the punters' choice for the victory. Much was made of Anthony Lynch's duel with Cooper as it was felt that Lynch had got the better of "The Gooch" in the season's earlier meetings. Lynch was booked early on for consistent fouling on Cooper who was the fulcrum of many Kerry attacks. Kerry eventually won an encounter 0-16 to 1-09, giving Cooper his fourth All Ireland Medal at 26.
In April 2010, Cooper sustained a serious eye injury in a NFL Division 1 win over Monaghan. He tore a duct in one of his eyes: doctors in Kerry expressed concern about his condition. He collided with Monaghan defender Darren Hughes after seven minutes and required treatment on and off the field. However, he returned to the Kerry team for the championship. After winning the Munster Championship, beating Limerick in the final, Kerry progressed to the All-Ireland quarter final, facing historic rivals Down. Despite a fine individual performance from Cooper, the Mournemen prevailed, thus preserving their 100% record against the Kingdom in the championship. The 2011 championship ended in final day disappointment for Cooper. Kerry, in control of the all Ireland final having been 4 points up in the closing minutes, succumbed to a quickfire blitz from rivals Dublin, who outscored the Kerrymen 1-3 to 1 point in the final stages to win the cup for the first time since 1995.
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