The DJ and TV presenter was asked by Radio 1 Breakfast Show host Nick Grimshaw to review his show today (October 3) during the changeover before her own weekday programme on the station.
"I thought it was good - Lily Allen seemed like she was in a good mood. She doesn't like me, but..." Cotton said.
Grimshaw asked: "Why doesn't she like you?"
Cotton said: "I dunno. Literally never spoke to her, but she has a pop at me. "
Grimshaw countered: "I think since she's had a baby, she's a changed woman."
Cotton said: "Really? I would love that to be proved. I've got no beef with her at all. I've met her like, once, but she doesn't like. I literally do not know why."
Grimshaw quipped: "She has a problem with everyone. That's part of her charm."
Cotton replied: "That's fine then! If that's what it is, that's cool by me."
Grimshaw said: "I've known her for about five years and it's touch and go if I get a reply off her on a text!"
Cotton continued: "She sounded in a really good mood, and I thought 'Aw, it sounds like she's having a really nice time with you'."
Grimshaw said: "It's cos the baby... once you have a baby you're going to be nice to people."
Cotton said: "Really? Is that going to happen? I look forward to this change of heart."
Grimshaw joked: "Fearne, you might go the other way! You might start wearing prom dresses and Nike Air Max and kicking people."
Cotton laughed: "I don't think I could get away with that somehow. Not at this age."
In 2010, Allen appeared to criticise Cotton in her defence of BBC 6 Music when the station was threatened with closure.
"If they close 6 Music, instead of acts like Seasick Steve and presenters like Lauren Laverne, it will be the Pussycat Dolls and Fearne Cotton on Radio 1," Allen said.
Allen later made a sarcastic comment about Cotton on Twitter, calling her a "trendsetter".
Cotton swiftly responded: "Not sure if lilyroseallen is being sarcastic or just nice? Thanks either way lilly."