The notoriously private star revealed the news during an interview on The Late Show with Stephen Colbert.
"I'm telling this for the first time, it feels so strange," she told the host. "I gave birth to a baby boy on September 3."
Colbert responded, "No one even knew you were pregnant!"
"I know," Mindy laughed. "This is news to a lot of people, it's true."
The actress revealed she had named her son Spencer.
Mindy is also mum to daughter Katherine Kaling, two, who she lovingly refers to as Kit.
Mindy has never spoken about who the father of her daughter – and now son – is, choosing to keep that a secret.
However, she has previously revealed that her former boyfriend and The Office co-star B.J. Novak is her daughter's godfather.
The actress has been very active on social media during the coronavirus pandemic, even sharing photos of herself in swimwear, which is how she seemed to trick us all.
The announcement comes just after the release of her second book Nothing Like I Imagined (Except For Sometimes), a collection of personal essays.
In the book, Mindy speaks about motherhood and the possibility of having more children after Katherine.
She revealed her baby nurse Rose helped her immensely after welcoming her daughter, "Rose helped me with everything. The fear of being alone with my baby. The fear of my baby not bonding with me. The fear of me not bonding with her. The fear of not being able to feed her... All these fears were the worst I've ever had in my life, and Rose helped me keep them at bay. She was my mom when I needed a mom, and that wasn't even her job."
She continued, "I told her I don't know if I'll have another baby, but if it meant she would come and live with me, I may just go ahead and do it."
Speaking about being a single mother Mindy also said, "Sometimes it's the most liberating and lucky feeling in the world."
"Sometimes I am just so grateful to be an independent woman doing what I want, when I want, that I could cry with gratitude."
Mindy has previously spoken about why she doesn't share photos of her daughter's face on social media, telling Glamour, "It's really essential to my life that there be something not everybody knows about. That's a boundary, but it's a very small boundary. Everything else I really don't have any issue sharing."