She broke the news in a black-and-white Instagram photograph of her bare stomach cradled by Thompson. A lengthy caption accompanied the photo, saying it was Khloe Kardashian's "greatest dream realized."
"We are having a baby! I had been waiting and wondering but God had a plan all along," she wrote.
Khloe Kardashian thanked Thompson for "making me a mommy."
"I still at times can't believe that our love created life! Tristan, thank you for loving me the way that you do! Thank you for treating me like a Queen! Thank you for making me feel beautiful at all stages!" her post read.
Though the baby will be Khloe Kardashian's first, Thompson already has a 1-year-old son with ex-girlfriend Jordan Craig.
In August, Khloe Kardashian, 33, told You magazine she and Thompson, 26, were waiting to have children.
"Tristan is a great dad and he definitely wants more children, but we both feel that it will happen when the time is right," she said.
"We're still in a new relationship and I love us having time together," the Keeping Up with the Kardashians star said. "Once you have kids you can't get back your non-kid years ... You worry about your children for the rest of your life."
My greatest dream realized! We are having a baby! I had been waiting and wondering but God had a plan all along. He knew what He was doing. I simply had to trust in Him and be patient. I still at times can't believe that our love created life! Tristan, thank you for loving me the way that you do! Thank you for treating me like a Queen! Thank you for making me feel beautiful at all stages! Tristan, most of all, Thank you for making me a MOMMY!!! You have made this experience even more magical than I could have envisioned! I will never forget how wonderful you've been to me during this time! Thank you for making me so happy my love! Thank you to everyone for the love and positive vibes! I know we've been keeping this quiet but we wanted to enjoy this between our family and close friends as long as we could privately. To enjoy our first precious moments just us ❤️ Thank you all for understanding. I am so thankful, excited, nervous, eager, overjoyed and scared all in one! But it's the best bundle of feelings I've ever felt in my life! ❤️❤️❤️
Khloe Kardashian and Thompson, who plays for the Cleveland Cavaliers, were first linked in October 2016 following their respective splits from James Harden and Craig.
Sources first reported Khloe Kardashian was pregnant in September, but the couple have waited to officially confirm the news.
"I know we've been keeping this quiet but we wanted to enjoy this between our family and close friends as long as we could privately," she said.
And last month, big sister Kim Kardashian, who's also expecting a baby via surrogate, coyly smiled when James Corden asked her point blank if her sisters were pregnant. Instead of answering the question, she opted to drink a sardine smoothie in a game on the late-night show called "Spill Your Guts or Fill Your Guts."