The presenter, who joined the show two years ago, will not return after the show's summer break.
Zoe Tyler, who has been a panellist for four years, will also exit the ITV1 programme as producers deal with a huge slump in ratings.
"'Kate and Zoe have been fantastic on Loose Women," an ITV spokeswoman told The Mail on Sunday. "We've really enjoyed working with them and look forward to working with them again in the future."
A show source added: "Contracts were signed on Friday and all the panellists who are returning have been spoken to. There will be some changes and it is true that Kate and Zoe will not be coming back in September."
Lynda Bellingham, Denise Welch, Lisa Maxwell and Carol McGiffin will all return as panelists, while former weathergirl Andrea McLean will remain in her role as anchor.
Coleen Nolan has already announced that she is leaving Loose Women to "move on to new adventures". Three newcomers are now expected to join the show.
Sarah Millican, who joined the panel at the beginning of the year, is said to be unsure of her return due to other commitments.
Thornton, who confirmed her split from fiancé Darren Emerson on Loose Women in February, was famously axed from The X Factor in 2007 and replaced with Dermot O'Leary.