The "With You" singer confirmed the news on Jan. 13 (Monday), in a statement to People.
"Eric and I have been living separately, navigating a painful situation in our marriage," the "With You" singer said.
"Our children come first, and we are focusing on what is best for them. We are grateful for all of the love and support that has been coming our way, and appreciate privacy right now as we work through this as a family," she continued.
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Simpson sparked rumors she and the retired athlete had called it quits last year after she was spotted sans wedding ring.
In November, the 44-year-old teased a "comeback" to her musical roots sharing snaps of her in a recording studio.
"Interviews in my Nashville music room where I unearthed my singular magic," she captioned the post on Instagram.
"This comeback is personal. It's an apology to myself for putting up with everything I did not deserve," Simpson added.
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The "Irresistible" singer and Johnson tied the knot in 2014 after four years together.
Simpson and Johnson share three children: daughters Maxwell "Maxi" Drew, 12, and Birdie Mae, 5, and son Ace Knute, 11.
The author was previously married to boybander Nick Lachey from 2002 to 2006.
Simpson and Lachey's marriage was documented in their MTV reality show, Newlyweds: Nick and Jessica.