McNicholas is replacing Michael Harvey who stepped down as editor in April to take up a freelance career, while continuing to act as an editor.
IPC, which owns NME, has yet to appoint a replacement for McNicholas, who has edited the music title since 2002. He will take up his new role within the next few months.
Prior to his stint at NME, McNicholas edited dance title Muzik, which closed in 2002, and has also held senior editorial roles at Mixmag magazine.
The departure of McNicholas comes as IPC publishing executive Faith Hill takes over as publisher of NME and its entertainment title, Uncut, with a brief to guide NME's multimedia expansion.
Under McNicholas's tenure, NME has attempted to make up for falling sales of the printed publication by aggressively expanding its digital services, including revamping its mobile site and launching a digital TV and radio channel.
NME's circulation was just over 73,000 when he joined the magazine and rose to more than 76,000 in 2005, but has trailed off in recent years.
According to the latest Audit Bureau of Circulations (ABCs) figures, the title's circulation dropped more than 24% year on year to record an average sales figure for July to December of 48,459.
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