He replaces the high-profile Anthony Noguera, who left Bauer Media last month to work on his own new ventures.
Kennedy, who is currently digital creative director at the German-owned publisher, will start his new role immediately.
He will, however, face a stern challenge in stemming the falling circulation of a magazine that in 1998 boasted a circulation of around 775,000.
Under Noguera, the title looked to reposition itself away from the lads' end of the market, but its circulation dropped by 13.5% year on year, to 272,545, in the last ABC figures for the year to December 2008.
However, FHM remains the market leading paid-for men's magazine, ahead of its nearest rival Men's Health, with 250,000.
Kennedy, who was editor of Empire for three years, is the sixth editor of FHM and follows in the footsteps of editors such as Ed Needham and Mike Soutar.