He will take responsibility for the magazine and all its editorial digital activities.
Noguera is a former editor of FHM, and remains editor-in-chief of Emap East, which includes titles Arena, Arena Homme Plus and Zoo.
Brown has left FHM after 10 years on the magazine, to "pursue other opportunities", according to the publisher. Brown had risen through the ranks from work-experience to editor.
In a statement to staff, Rob Munro-Hall, managing director of FHM, Emap East and Emap Metro, said he "would like to thank Ross for his extraordinary contribution to the FHM story and wish him the very best of luck in the future".
Ben Todd has been appointed editor at Zoo, taking over Noguera's responsibilities.
Todd joined Emap as deputy editor of Zoo earlier this year from the Sunday Mirror, where he had been assistant editor for three years.
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