In scenes to be aired at the end of summer, Kat (Jessie Wallace) will discover that she's pregnant with Alfie's baby, despite him believing he's infertile.
She then falls ill and is rushed to hospital, where she is told the devastating news, the Daily Star Sunday reports.
"The pregnancy takes Kat and Alfie (Shane Richie) completely by surprise and neither of them know how they really feel about it," a source said. "Kat is understandably very nervous and anxious about having another baby.
"Her head is all over the place. But before she has a chance to get used to the idea she suffers a miscarriage. It is a cruel thing to happen to them after everything that they've already been through this year.
"And once again viewers will be in tears as they watch Kat come to terms with losing her baby."
Kat was at the centre of the baby swap storyline earlier this year, when Ronnie Branning (Samantha Womack) lost her son James to cot death before switching him with Kat's healthy newborn Tommy. The plot received record viewer complaints.
An EastEnders spokesperson added: "There is a little bit more heartache for Kat and Alfie as they try to rebuild their lives with Tommy."