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The former couple, whose on-off relationship has been documented on The Kardashians, also have a four-year-old daughter named True.
Kardashian and Thompson have not yet decided on a name for their son, according to reports in the US media.
News of the pregnancy first broke in July, with a representative for Kardashian describing it as a “beautiful blessing” at the time.
“We can confirm True will have a sibling who was conceived in November,” the statement said.
“Khloé is incredibly grateful to the extraordinary surrogate for such a beautiful blessing. We’d like to ask for kindness and privacy so that Khloe can focus on her family.”
The timeline suggested that the decision to conceive the baby would have been taken before it was revealed in December 2021 that Thompson had been unfaithful to Kardashian and fathered a child with personal trainer Maralee Nichols.
Court documents showed that Thompson slept with Nichols in March 2021, while he was in a relationship with Kardashian.
Reading the court documents while on the phone to her older sister, Kim, Kardashian is heard saying: “What the f*** is this?”
She also tells half-sister Kendall Jenner that she “wanted to believe that Tristan could change”. “I wanted to trust him,” she added.
Kardashian and Thompson first began dating in 2016 but have had a tumultuous relationship due to Thompson’s repeated infidelity.
In 2018, TMZ published video footage of Thompson kissing a woman at a hookah lounge in Washington DC. TMZ claimed the footage was recorded in October 2017, while Kardashian was pregnant with True.
Later in 2019, Keeping Up With The Kardashians documented the Good American Founder’s reaction after finding out that Thompson had kissed sister Kylie Jenner’s friend Jordyn Woods at a party.
In January this year, Thompson issued a public apology to Kardashian via Instagram, writing that he takes “full responsibility” for having a child with Nichols.
“Khloe, you don’t deserve this. You don’t deserve the heartache and humiliation I have caused you,” he said.
“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.”