Moynihan will join IPC as digital editor for NME and Uncut on October 1. He joined FHM in 2000 as a staff writer, and climbed the ranks to deputy editor of the website in 2004, before a promotion to editor earlier this year.
Moynihan is replacing Ben Perreau who now works with Sony and will report directly to the editor of NME, Conor McNicholas.
FHM.com gained a community section under Moynihan's leadership, and he prioritised video, user-generated content, and e-newsletters, which helped drive traffic and advertising revenue.
Paul Cheal, IPC Ignite publishing director, said: "His experience at FHM coupled with his passion for both music and the NME makes him the perfect choice for this role."
Moynihan said: "Ignite's music brands are internationally famous -- and rightly so. To have the chance to work with their award-winning teams to drive online development to the next level is pretty much a dream come true."
It is not known who Emap will appoint to manage the FHM online team following Moynihan's departure.
IPC Ignite is the home of NME, Nuts, Loaded and Uncut magazines. NME.com last week announced a deal with iTunes to offer free video downloads.
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