TMZ reported that the 35-year-old golfer submitted a three-page document to a court in Florida on May 13. The reason for the divorce was not disclosed.
The Northern Irish star has proposed keeping the prenuptial agreement as well as implementing a joint parenting plan.
McIlroy's team released a statement to multiple media outlets, asserting McIlroy's desire to ensure this difficult time is as respectful and amicable as possible and that he will not be making any further comments on the matter at this time.
The surprised split from his wife came in the days between him winning the Wells Fargo at Quail Hollow on Sunday and the start of the PGA Championship at Valhalla on Thursday.
The couple met when McIlroy overslept at the 2012 Ryder Cup and Stoll, who was managing the volunteers for the tournament, arranged a police escort to get him there in time.
At that time, McIlroy was still dating Danish tennis star Caroline Wozniacki. They called off their engagement in 2014.
In 2015, McIlroy and Stoll started dating and he proposed in December that year. The couple kept their relationship low-key. They tied the knot in 2017 and welcomed their daughter Poppy three years later.
McIlroy, 34, has been the number one golfer in the world nine times since 2012, winning 26 PGA Tour titles.
He is currently ranked fourth on the list of athletes with the most number of weeks at number one with 122 weeks.