Smith was executive editor of Arena prior to taking charge on a temporary basis when Giles Hattersley left in March after one year to return to The Times.
A Bauer spokeswoman said a successor to Smith would be announced "shortly" and Anthony Noguera, group editor-in-chief of FHM and Arena, is in charge in the interim.
When he joins Esquire on September 1, Smith will take over the features director role from Shaun Philips. Philips has been recruited by The Times as associate features director.
Jeremy Langmead, editor of Esquire, said: "Mat has years of experience on men's magazine and a sharp and sophisticated eye for a strong feature and the right writer.
"I've been a fan of Mat's work and envious of many of his story ideas for a long time."
Arena's average circulation has dropped to a low of 25,232 copies according to the magazine ABC figures for July-December 2008. This is down 18.3% over six months and down 27% over a year.
Esquire's circulation is 59,800, which is up 11.7% over six months and up 14% over a year.
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