Though the baby will be Kardashian's first, Thompson already has a 9-month-old son with ex-girlfriend Jordan Craig.
"Yes, Khloe and Tristan are expecting and they are absolutely thrilled," a source told People Magazine. "This isn't something they were in a rush to announce to the whole world, and it's only been in just the past week or so that they've felt comfortable telling most of their inner circle.
Another source told E! News that "Khloe is so happy you have no idea."
In August, 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."