McNicholas took over the publication in June 2002 and was named PPA consumer editor of the year in 2004 and BSME editor of the year for entertainment magazines in 2005.
Publishing director Paul Cheal said: "Conor has made a great contribution to the ongoing development of the NME."
McNicholas said: "It's been a huge privilege to edit the NME and be part of such an iconic brand that has continued to shape the future of magazine publishing."
On his Twitter page, he added: "I'm leaving to go and edit Top Gear magazine at the BBC. Amazing job for a petrolhead like me. Will be at NME for a good few weeks yet."