Morten Madsen was drafted by the Minnesota Wild in the 4th round, 122nd overall, in the 2005 NHL Entry Draft. After being drafted, Madsen joined the Victoriaville Tigres of the QMJHL for the 2006–07 season. In his lone season in the QMJHL he registered 32 goals and 68 assists for 100 points in 62 games. In six playoff games with the Tigres he scored 3 goals and added 6 assists in six games. Before entering the QMJHL he played for Frölunda HC's junior team in Sweden. Prior to moving to Sweden he played junior hockey for Danish Rødovre Mighty Bulls as well as two games for Rødovre's senior team at the age of 15.