Karlsson turned professional in 1989 and qualified for membership of the European Tour at the 1990 Qualifying School. Since then he has retained his card and has had a consistent career on tour. The highlight of his career came in 2008 when he won the Order of Merit. He has finished in the top twenty of the Order of Merit six times throughout his career and has won nine events on tour.
2006 was a good year for Karlsson, at the Celtic Manor Wales Open, he broke the European Tour's 36 hole and 54 hole scoring records by shooting 124 for the first two rounds and 189 for the first three. However as the course was a par 69, which is rare at the top level, his to-par scores were a much less remarkable 14 under after two rounds and 18 under after three. His second victory of 2006 at the Deutsche Bank Players Championship of Europe in July helped him reach the top 50 of the Official World Golf Rankings.
In 2008 Karlsson entered the top 25 of the Official World Golf Rankings. His win at the Alfred Dunhill Links Championship took him to number 8 in October 2008. A T3 finish at the Portugal Masters two weeks later took him to number 6. He has spent over 25 weeks in the top-10 since 2008.
Karlsson was a member of the Continental Europe team in the Seve Trophy in 2000, 2002 and 2007. In 1999 he was eleventh on the Ryder Cup qualifying table just missing out on the last automatic place, and was not selected as a captain's pick. He made his Ryder Cup debut in 2006, at the age of 37, along with fellow Swede Henrik Stenson. He played again in 2008, forming a partnership with PÃ¡draig Harrington in the foursomes and beating Justin Leonard 5 & 3 in the singles on Sunday.
After a strong finish to the season, Karlsson won the Order of Merit in 2008, being the first Swedish golfer to do so. Because the name of the money list changes to the "Race to Dubai" beginning with the 2009 season, it was the final "Order of Merit" win. This achievement, among other things, resulted in him winning Swedish male athlete of the year at the Swedish Sports Gala in January 2009, also a Swedish male golfer first.
In June 2009, Karlsson suffered from an eye injury, with no depth-perception in his left eye. It happened during the week of the St. Jude Classic, the week before the U.S. Open, which Karlsson was set to play in, teeing off in the first round with fellow Swede Henrik Stenson. The eye injury caused Karlsson to withdraw from the event and he missed most of the rest of the 2009 season. He returned for The Vivendi Trophy toward the end of the season, and completed his recovery by claiming his tenth Tour title at the 2010 Commercialbank Qatar Masters the following January. In June, Karlsson lost in a sudden death playoff to Lee Westwood at the St. Jude Classic.