Bakke was bought by Leeds United in 1999 from Sogndal for £1.75 million. After an encouraging start to his career at Leeds in 1999 and 2000, injuries and poor form meant that he never quite became a mainstay of the Leeds squad, even after the club was relegated from the Premiership in 2004. Bakke's career has been blighted by recurrent knee injuries. Patella tendinitis kept him out of the team for the start of the 2004-05 season and he was struck with a torn cruciate ligament on his return in January 2005. In August 2005, having recovered from his injury, Bakke was loaned to Aston Villa. The loan however was ended early after Leeds told Villa that they would only let Bakke go permanently, not on loan and Doug Ellis, Villa's chairman at the time, decided that it was not worth permanently acquiring his services. Speculation continued as to Bakke's future when he was left out of the Leeds United squad for the match against Sheffield Wednesday on 27 August 2006 with some in the press and supporters speculating that this was due to an imminent transfer. A club statement was released on 29 August 2006 by Leeds United effectively stating that Bakke had played his last game in Leeds United colours. Bakke however stated he would like to stay at the club, and still trained with the club, despite not playing, not wanting to return to playing in Norway at that point in time. The problem arose due to his £23,000 a week wages and £4,000 appearance fees, which were originally agreed during Ridsdale's "Living The Dream" era, but which the club could no longer afford to pay in the league they were currently playing in. Leeds United tried to resolve the issue by attempting to meet Bakke half way so that the player could stay at the club on lesser wages but Bakke's agent stated he wanted the contractually agreed wage. The situation did not look good for Bakke, with Leeds chairman Ken Bates having already terminated Seth Johnson's contract due to excessive wages as part of a determined effort to make Leeds a successful and profitable club once more. Bakke left, being the third last 'O'Leary player' left at Leeds.
On 31 August 2006, Bakke signed a two-year deal with SK Brann, and returned home to Norway. The deal was financed by Hardball. Certain media outlets have claimed that Bakke and Brann have a "gentlemen's agreement", that Bakke can leave Brann if a big club wants to sign him, though this has been denied by Brann. Bakke has stated that he still has ambitions to prove himself in Europe before bringing his career to a close in Norway. Bakke debuted for Brann on 11 September 2006 against Stabæk, in a match best remembered for a two-feet tackle by Joakim Persson of Stabæk on Bakke that could easily have ended Bakke's career. Bakke started the 2007 season playing for Brann 2 in a bid to regain full fitness from his injury problems. He has experienced a bit of a stop-start season, making his first full Tippeliga start on 26 June 2007. Eirik Bakke has been mostly noticed for his no-nonsense approach and English inspired tackling in midfield, but also managed to score the winning goal against arch-rivals Rosenborg BK on 11 August 2007. Bakke has promised Brann that when he is close to retirement he would finish his career in Norway with the club, playing a further 1-2 seasons. In front of the 2008 season, Bakke became captain of Brann. On 30 May 2008, Bakke extended his Brann deal out 2010. However his new deal had a clause giving Bakke the chance to re-evaluate his deal, if the club decided to lay artificial turf at Brann Stadion. A few weeks later, Brann announced that the club will continue with natural grass as the turf at Brann Stadion also in the coming years.
Sogndal (2011-2012)
He signed a two-year deal with Sogndal in 2011. In November 2012 he decided to retire as an active player.