Kennedy succeeds Anthony Noguera, who was editor of FHM and editorial director of Bauer's men's lifestyle magazines before leaving the company in April. He joined FHM in 2007.
Geoff Campbell, managing director of Bauer Media men's lifestyle division said: "Colin brings a wealth of big brand editorial experience, an impressive track record of innovation and editorial product development, a proven digital ability and a deep understanding of FHM's audience that will prove invaluable to the continued evolution of this most famous of men's lifestyle brands."
Kennedy was editor of film magazine Empire for three years from 2002, delivering record sales of more than 205,000 copies.
He said: "Ever since I supplied the odd article to FHM's Reporter section back in 1997, I have waited for a chance to contribute to the worldwide success story of Bauer's flagship men's title.
"That this opportunity turns out to be as editor during such an important time for the brand is genuinely thrilling -- and just a little bit scary. Hopefully, some of the things I've learned along the way will help me take the team and the title forward into a new decade of success."
FHM is currently the most popular paid-for men's magazine by average issue circulation, with 272,545 copies.
However, its circulation is down by 13.5% over a year while that of nearest rival Men's Health climbed by 4.1% to reach 250,094, closing the once distant gap between the two.
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