The Keeping Up With the Kardashians star made the announcement on Instagram on Sunday, posting a black and white photo of the newborn's hand being held by her daughter, Stormi.
She has not yet announced the baby's name.
Jenner captioned the photo with a blue heart, indicating she has had a son, along with the date, "2/2/22", suggesting he was born four days before she made the announcement on February 6.
The baby boy is Jenner's second child with rapper Travis Scott, 30. The couple have a daughter, Stormi, 4, who celebrates her birthday one day before her new brother, on February 1.
Before announcing her son's birth, Jenner celebrated Stormi's birthday with an Instagram post with the toddler in Scott's arms. It was captioned: "Our baby is 4 ... happy birthday to the girl that changed my whole world."
Jenner is the youngest of the Kardashian-Jenner siblings. She is behind the Kylie Cosmetics beauty company and is currently the most-followed woman and the second-most-followed person, behind Cristiano Ronaldo, on Instagram.
In September she launched her own family-friendly line of "clean, vegan" baby products with Kylie Baby.
"We put so much love into this, we have been working on it for what seems like for ever at this point and it was just such a dream to do clean, vegan baby products for you guys, that I'm obsessed with," Jenner, 24, said on her Instagram Story.
On November 5, Jenner was at the tragedy-stricken Astroworld Festival, where 10 people were killed after a crowd surge. The music event was founded by her rapper partner, Scott, and the deadly surge took place when he was performing on stage.
Jenner said she was "devastated" by the deaths.
"Travis and I are broken and devastated. My thoughts and prayers are with all who lost their lives, were injured or affected in any way by yesterday's events," she wrote in a post on Instagram.
"I want to make it clear we weren't aware of any fatalities until the news came out after the show and in no world would have continued filming or performing."