The long-awaited appointment will see Duncan Wingham take up the post for a four-year term, starting on 1 January 2012.
The position has been filled by interim chief executive Steven Wilson since July, when Alan Thorpe moved to the European Centre for Medium-Range Weather Forecasts.
Professor Wingham, who will also serve as the Nerc’s deputy chair, is professor of climate physics at University College London, and the founder and former director of the research council’s Centre for Polar Observation and Modelling.
An expert on the behaviour of the Antarctic and Arctic ice sheets and sea ice, he said it was “an honour” to head up the council.
“Environmental science lies increasingly at the heart of many of the challenges and opportunities that face us today, and Nerc must continue to play a leading role in developing this science, and ensuring the widest possible impact of its work,” he said.
David Willetts, the universities and science minister, said Professor Wingham’s knowledge and expertise would be “vital in leading an organisation that funds world-class science and increases knowledge and understanding of the natural world”.