World number two McIlroy made the filing a day after winning his 26th career US PGA Tour title at the Wells Fargo Championship and a day before working Tuesday at the PGA Championship at Valhalla on the practice range just after celebrity website TMZ broke the news.
McIlroy, a 35-year-old from Northern Ireland, and top-ranked Scottie Scheffler, are favored for the title this week.
McIlroy, a four-time major champion, won his most recent major title at Valhalla a decade ago at the PGA Championship.
Documents filed in Palm Beach County, Florida, confirmed the move by McIlroy, whose communications team said in a statement that McIlroy wanted "to ensure this difficult time is as respectful and amicable as possible" and that he would make no further comment.
McIlroy is set to speak with the media on Wednesday afternoon, barely 17 hours before his morning start Thursday alongside Dustin Johnson and Justin Rose at Valhalla.
Erica Stoll was working for the PGA of America when she met McIlroy in 2012 at the Ryder Cup and they began dating in 2015, becoming engaged in December 2015 while on holiday in Paris and marrying in April 2017 at an Irish castle.
Their three-year-old daughter, Poppy, was born in 2020.
McIlroy had previously dated Danish tennis star Caroline Wozniacki from 2011 to 2014. They became engaged on December 31, 2013, but McIlroy announced in May 2014 that he had ended the engagement -- then won the same week at Wentworth on the European Tour.
McIlroy went on to win the 2014 British Open, the WGC Bridgestone Championship at Firestone and the PGA Championship, his most recent major triumph.
He enters having won his past two PGA Tour starts, a pairs event last month in New Orleans alongside Ireland's Shane Lowry and his fourth career triumph at Quail Hollow on Sunday.
After his Mother's Day triumph, McIlroy praised his mom, Rosie, but did not mention his wife and said only of his plans that he would "probably go home and reset" in Florida before coming to Valhalla.
McIlroy is among the members of the PGA Tour Policy Board transactions subcommittee that is negotiating a merger deal with Saudi Arabia's Public Investment Fund (PIF). He quite the board last year hoping to spend more time on improving his game.
McIlroy said after his victory at Quail Hollow that playing golf was "a nice escape from everything that's going on in the world of golf."
"I've always been able to compartmentalize pretty well. I seem to, for whatever reason, play very good golf whenever I have a lot of stuff going on," McIlroy said.
"I don't know if I need that just to really, when I get on the course, focus on what I'm doing out there, but it seems to work."
