Karlsson, still hired by Frölunda, took a leave of absence prior to the 2006–07 season and signed a contract with Linköpings HC as assistant coach to Gunnar Persson.

[2] Persson was fired in January 2007 and Karlsson took over the job as head coach,[5] he led Linköping to the Swedish Championship finals where they lost two games to four against Modo Hockey.

After the 2010–11 season, Karlsson left HV71 and signed as assistant coach to Bengt-Åke Gustafsson in the Atlant Moscow Oblast of the Kontinental Hockey League (KHL).

[6] After a disappointing start of the 2011–12 season for Moscow Oblast, Karlsson took over the head-coaching job for the team as Gustafsson was forced to leave the club.

In September 2005 Karlsson was announced as a permanent assistant coach to Gustafsson,[13] he participated in all the 2005–06 Euro Hockey Tour tournaments except for the Rosno Cup.

[15][16] Karlsson together with Boustedt and Samuelsson were assistant coaches to Gustafsson at the 2007 World Championship,[11] where Tre Kronor lost to Russia in the bronze medal game.

Following the World Championship Karlsson announced that he resigned from his permanent position with Tre Kronor due to his obligations as head coach of Linköping.