Kennedy was most recently the digital creative director with Bauer, after being appointed to the role in 2006.
Kennedy joined Empire in 2000 and become the editor in 2002. Under his editorship, the magazine marked the release of the final Star Wars movie with an edition carrying the sound effect of Darth Vader’s deep breathing when opened.
Noguera, who was also the editorial director across men’s lifestyle, left the company in April after 14 years.
During his editorship, FHM repositioned away from the lads end of the market.
Geoff Campbell, the 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 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 be as editor during such an inportant 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."