Hughes, who is also chairman of Emap Performance, the radio, TV and Q and Mojo music magazines division, has been group finance director for five years.
Tom Moloney, chief executive of Emap, said: "Gary leaves the business in good financial shape. His desire now to look for broader career opportunities elsewhere has my full support."
Emap's recent trading update ahead of its 2004 results showed that group revenues rose 2% year-on-year despite difficult trading at Emap France.
Hughes is also currently a non-executive director of Sainsbury's. Positions he held prior to joining Emap include group finance director of Scottish Media Group, deputy finance director of Forte and a number of senior management positions at Guinness.
Hughes said that he intended to take a short career break over the summer and then pursue opportunities elsewhere.
Emap is yet to fill another senior position, that of managing director of Emap Advertising, which was vacated by Dave King's move to the Telegraph Group in January.
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