Emap said Middleboe's departure would allow it to further invest in products and increase its revenues.
His responsibilities will be subsumed into the remit of Emap chief executive David Gilbertson, who told Media Week its publishing division was performing strongly despite the departure.
Gilbertson added he had no immediate plans to recruit a replacement for Middleboe, who has spent more than 25 years with the business.
Emap's business-to-business unit was acquired by Guardian Media Group and private equity firm Apax at the end of 2007.
The business was subsequently split into four divisions, including Emap Inform, which publishes an array of titles including Retail Week and Broadcast, and was headed by Middleboe.
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