The golf star announced the birth, revealing they have named their daughter 'Poppy Kennedy McIlroy'.
The baby was born at 12.15pm on Monday and McIlroy described her as "the absolute love of our lives".
He also shared a picture of the baby's hand.
He wrote: "Poppy Kennedy McIlroy, born August 31st, 12:15pm. She is the absolute love of our lives. Mother and baby are doing great. Massive thank you to all the staff at Jupiter Medical Center and Dr Sasha Melendy for their amazing care."
Poppy Kennedy McIlroy, born August 31st, 12:15pm. She is the absolute love of our lives. Mother and baby are doing great. Massive thank you to all the staff at Jupiter Medical Center and Dr Sasha Melendy for their amazing care ❤️❤️❤️ pic.twitter.com/IwFeGf8rod
— Rory McIlroy (@McIlroyRory) September 3, 2020
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News emerged that the couple were expecting their first child last weekend.
While McIlroy was competing at the BMW Championship in Illinois, golf pundit Steve Sands let slip that his wife was at home as their first child was due "any day now".
McIlroy had said he was willing to withdraw from the tournament, or the upcoming Tour Championship, if Stoll went in labour.
It remains to be seen if the defending champion will compete at East Lake when play gets under way on Friday, although he is no longer scheduled to give an interview on Thursday afternoon.
McIlroy (31) and Stoll married in a lavish reception at Ashford Castle in Co Mayo in 2017.