Kazakhstan Cup 2009 was the 18th season of the annual nationwide cup competition of Kazakhstan since the independence of the country. The competition started on 24 April 2009 and ended on 15 November 2009. In the final, Atyrau beat Shakhter to win its first cup and earn a place in the second qualifying round of the UEFA Europa League 2010–11.
All 28 teams from both the Premier League and First Division entered in this round. The draw was conducted on 26 March 2009 at the offices of the Football Federation of Kazakhstan. For every match, one First Division team was drawn against one Premier League team, with the First Division team assigned as the home team. The exception was a match between Shakhter and Ekibastuzets which was played at Shakhter's pitch due to insufficient pitch conditions in Ekibastuz. The matches were played on 24 and 25 April 2009.
The draw was conducted on 29 April 2009 at the offices of the Kazakh Football Federation. The fourteen winners of Round 1 were drawn into six matches. Thereby, Zhetysu and Atyrau received a bye. The first legs were played on 20 May 2009 while the second legs were played on 23 June 2009.