Konerko told ESPNChicago.com that he will opt for the surgery, which will remove the particle that floats between the hand and left wrist area.
"It is something I need to take care of," Konerko said. "I don't feel it has impacted anything I've done this year. It is just time to get it out of the way."
Chicago's captain, Konerko said he's had the fragment in his hand since 2009, and has had occasional shots and treatment when it's flared up.
Konerko said the recovery time after the procedure is likely four to six weeks.
Konerko signed a three-year, $45 million contract extension in December 2010. The 36-year-old veteran has been an iconic player with the White Sox, hitting his 400th career home run in his 13th year in Chicago.
Like many of his teammates, Konerko has slumped in the last two weeks, going 7 for 46 (.152 ) in his last 13 games entering Sunday.