It is understood the decision for Gilbertson's departure was reached "mutually" yesterday with Emap's joint investors, private equity group Apax Partners and Guardian publisher Guardian Media Group.
The company said it expects to give an update on its succession plans "in due course".
Emap's offering spans magazines including Construction News and Retail Week, events such as the World Architecture Festival, and intelligence services such as fashion-focused WGSN.
It is believed the company's 2010 financial results due out in the next two months will show the business is performing well.
Between 2008 and 2009 the company's revenues dropped from £283m to £282m but it turned a pre-tax loss of £2m into a pre-tax profit of £34m.
Irina Hemmers, a partner at Apax Partners, who chairs the board overseeing Emap, said: "David has led Emap with distinction over the last three years. He leaves the business in good shape and well placed for growth. The shareholders are grateful for his contribution and he goes with our best wishes for the future."
Gilbertson said: "It has been my complete privilege to lead Emap for the last three years. It is a first-class business with some of the strongest brands in all B2B. It has proved to be highly resilient through the challenges of recession and is now on target to return to growth this year.
"Recession has extended the likely period of private equity ownership for the business, making this an opportune moment for new leadership to take the company on to its next phase. I wish Emap, its staff and its shareholders every success as the business continues to progress."