The ex-Swansea City star is believed to have been dumped by the Coronation Street actress after it emerged that he was allegedly sending flirty texts to TV presenter Donatella Panayiotou.
"I've always been deeply in love with Scott and the past few weeks have been heartbreaking," Flanagan told The Sun.
"I want to work things through and get back together. I just want to be happy again. We're spending time apart to sort things out, but my feelings for him have not changed."
The couple have been in a relationship for the last four years.