The NBA player, 30, delivered a message to Kardashian, 37, on his Instagram Stories Monday, where he also confirmed he fathered a child with another woman.
"Today, paternity test results reveal that I fathered a child with Maralee Nichols," Thompson wrote, adding that he takes "full responsibility" and plans to "amicably" raise his son with Nichols.
"I sincerely apologize to everyone I've hurt or disappointed throughout this ordeal both publicly and privately," he continued.
Thompson went on to apologize to Kardashian directly, writing that the reality star doesn't "deserve this."
"You don't deserve the heartache and humiliation I have caused you," he continued. "You don't deserve the way I have treated you over the years. My actions certainly have not lined up with the way I view you. I have the utmost respect and love for you. Regardless of what you may think. Again, I am so incredibly sorry."
USA TODAY has reached out to Kardashian's reps for comment.
Kardashian and Thompson's tumultuous relationship, which began in 2016, has played out across headlines and on the "Keeping Up with the Kardashians" reality show, which aired its series finale on E! in June.
Days before the couple's daughter True arrived in 2018, TMZ and Daily Mail published photos and video of a man identified as the basketball star kissing and fondling various women. One video was shot that April inside a Manhattan club. Another, picturing two women kissing and groping him, was filmed in October 2017 in Washington, D.C.
Reports of the demise of Kardashian and Thompson's relationship surfaced in 2019, as outlets linked Thompson to model Jordyn Woods, a close friend of Kardashian's younger sister Kylie Jenner.
In a March 2019 interview on "Red Table Talk," Woods, then 21, admitted she and Thompson kissed but denied speculation that she was the reason Kardashian and Thompson broke up.
"I know I'm not the reason that Tristan and Khloé are not together," Woods said. "This situation may have made it harder for her to want to be with him, but I know I'm not the reason."
Kardashian thought differently. She took to Twitter following the episode, accusing Woods of being the reason her family "broke up."
"Why are you lying @jordynwoods ?? If you’re going to try and save yourself by going public, INSTEAD OF CALLING ME PRIVATELY TO APOLOGIZE FIRST, at least be HONEST about your story."
Kardashian later walked back her comments, admitting she was going through a rough time and felt humiliated by the rumors but apologized for blaming Woods.
"What’s been harder & more painful is being hurt by someone so close to me. Someone whom I love & treat like a little sister," she added. "But Jordyn is not to be blamed for the breakup of my family. This was Tristan’s fault."
Thompson also a shares 5-year-old son Prince with model Jordan Craig.
Contributing: Erin Jensen, Hannah Yasharoff
This article originally appeared on USA TODAY: Tristan Thompson apologizes to Khloe Kardashian after fathering child