The 29-year-old, who turned pro in 2007, said following May's French Open he had swelling and fluid in the elbow and confirmed Monday that he would be receiving surgery to address the issue, reports Xinhua news agency.
On Tuesday evening, he underwent surgery at a hospital in Tokyo.
The Shimane Prefecture-born star, currently ranked 8th in the world, will begin post-surgery rehabilitation on Thursday, according to his management company.
It said he would likely return to full training in the earlier part of December, with an aim for him to return to the pro circuit next season.
Despite Nishikori hoping to play at one of the indoor competitions in Europe ahead of the November 10-17 Association of Tennis Professionals Tour (ATP) Finals, he said that the pain in his elbow was hampering his performance.
In September, Nishikori, the only male Japanese tennis player ever to be ranked inside the top 5 in singles, heard from his doctors that he would not be able to swing a racket for about four weeks.
After bowing out of the US Open in August in the third round, Nishikori, who beat Rafael Nadal to win the bronze medal at the 2016 Summer Olympics in Rio de Janeiro, announced in a Twitter post on October 15 that he will part ways with longtime coach Dante Bottini.
Nishikori, who added Michael Chang to his coaching staff in 2014, did not announce any changes in this partnership.
In his time away from the tour he has missed playing in the Rakuten Japan Open in Tokyo and the Shanghai Masters in China.
( With inputs from IANS )