The 'How I Met Your Mother' actor – who previously hosted the awards in 2009 – will take over for the ceremony on September 26 this year, just a few months after he presents the Tony Awards in June.
He said: “I couldn't be more honoured and excited to be hosting this year's Emmy Awards. And what perfect timing - I'll just do the exact same script I'm about to use for the Tonys. 'And the Emmy for Best Revival of a Musical goes to Breaking Bad!' See, told you it works."
CBS Entertainment chief Nina Tassler added: "Neil is the quintessential host - engaging, entertaining and a true showman - with a passion for celebrating the medium we all love. We're thrilled for him to return for CBS's broadcast of the Emmy Awards."
Neil has hosted the Tonys twice, with one stint in 2009 earning him and the production team an Emmy Award.
The 38-year-old star - who shot to fame as the titular character in hit TV series 'Doogie Howser, M.D.' - is also established on Broadway and has had roles in the play 'Proof' and the musicals 'Cabaret' and 'Assassins'.