Cotton took a short break from the programme in 2013 whilst on maternity leave and so during the ninth series, Kelly Brook stood in for her. In 2012, Cotton hosted The Nation's Favourite Number One Single, a three-part series, revealing Britain's Favourite No. Since 2016, Cotton has co-presented Fearne & Gok: Off The Rails, alongside Gok Wan for ITVBe.She also presented the Isle of Wight Festival 2009 on ITV2 alongside Rufus Hound. In 2003, Cotton moved over to mainstream broadcasting.She along with Simon Grant (her co-presenter from The Saturday Show) presented the spin-off show Top of the Pops: Saturday (later renamed Top of the Pops: Reloaded) that year.In 2004, she moved up to work alongside Reggie Yates on the main programme, Top Of The Pops (the then flagship chartshow for the BBC) becoming one of the last regular presenters for that programme, which ended in July 2006.
a skill she made much use of whilst presenting the series Draw Your Own Toons.
In 2007, she became the first regular female presenter of the Radio 1 Chart Show, which she co-hosted with Reggie Yates for two years.
She went on to present her own Radio 1 show, airing every weekday morning since 2009. In 2007, Cotton presented The Xtra Factor, an ITV2 spin-off from the main show.
From 2001 until 2003, she presented Finger Tips, an arts and crafts programme for children, which she co-presented with Stephen Mulhern.
She later co-presented on CBBC's Sunday morning show, Smile and on The Saturday Show.
In August 2017 Cotton's ancestry was explored in the UK BBC TV series Who Do You Think You Are?