The slightly-built rookie teenager was recruited by AFL club Port Adelaide in the 2006 AFL Draft. He was the player the Power was most surprised to be able to pick when it grabbed him at number 39. Krakouer shone at the 2006 AFL Draft camp in Canberra, setting a sizzling time in the 20 metre sprint on the second day of the camp. His time of 2.83 seconds puts his result in the top handful of all time, out of nearly a thirty players over the last 12 or 13 years. Wearing the number 29 guernsey, he has played 11 games for Port in his debut 2007 AFL season, despite coach Mark Williams earlier predicting that he would not play for at least two years. As at the end of round 7, he had an impressive total of 48 kicks, 24 marks, 18 handballs, 66 disposals and 4 goals. His explosive speed and raw talent has been progressively emerging throughout the season. Notably, he played a crucial role in securing a win over North Melbourne in round 2, with a significant hand in three Port goals in 15 minutes; three such goals being in the last five minutes of the game. Krakouer was also the only Power player to take more than one inside-50 mark in Port's loss to the Crows in Showdown XXII. At the end of round 7, Krakouer was ranked sixth among the AFL Rising Stars in total kicks and total marks, and seventh in total goals. In 2008, Krakouer managed just three games for the Power due to recurring soft tissue injuries, and was granted permission by the club to return home to Western Australia after suffering a season-ending hamstring strain in round 15. This led to speculation that Krakouer would seek a potential trade to the Fremantle Football Club or West Coast Eagles, two West Australian based clubs. However this never happened, with Krakouer stating: "I had a talk to Choco and I just couldn’t do it. I couldn’t tell him I wanted to go back. I felt like I couldn’t just walk out and I’m glad I didn’t." In 2009, an improvement in fitness and bulk in Krakouer saw him move to the backlines playing as a "sweeper role" and essentially replacing Peter Burgoyne who returned to his original position as a midfielder. Krakouer played well in this role, averaging over 20 possessions in the 2009 NAB Cup, and being named in the Power's round 1 game of the season. Season 2010 was forgetful for Krakouer as he was limited to just seven games due to injuries and lack of form.
On 1 September 2010, Krakouer signed a three-year deal with the Gold Coast Suns. He was the second uncontracted player to do so following Nathan Bock who left Adelaide. He left despite the disappointment of Port Adelaide who stated that given the commitment our football club has made to Nathan's development and welfare over the last four years, we are very disappointed at the way the matter has been handled in recent weeks. It was alluded to that Krakouer had already made the decision to leave Port Adelaide during the season, further highlighting criticism of the AFL's clause for the expansion teams ability recruit one uncontracted player from each of the 16 existing clubs. In December 2011, Krakouer was released by the Suns due to "personal reasons" despite being contracted to the end of the 2012 season.
Return to Port Adelaide (2015–2017)
On March 31, Krakouer was signed to play for the Port Adelaide Magpies in hope to re-ignite his AFL career. He polled best and fairest votes in 12 of his 16 games, and was subsequently drafted as a rookie by Port Adelaide's AFL side. Starting on the rookie list in 2015, he impressed in the pre-season trial matches and was quickly promoted from the rookie list to play his first AFL game for the Power since 2010 in round 3 as his accurate kicking and smooth movement off the half back line proved to be valuable. He played 7 games before being returned to the rookie list. He was immediately reinstated to the senior list as a mid season promotion and went on to play another 7 games for a return of 14 on the season. At the conclusion of the 2017 season, Krakouer announced his retirement from AFL football.
