Iain Lobban, 53, will leave the agency later this year after serving nearly six years as director, the Foreign Office said.
It denied that his departure was related to revelations contained in Snowden's leaked documents that GCHQ was one of the main players in mass telecommunications surveillance.
"Today is simply about starting the process of ensuring we have a suitable successor in place before he moves on as planned at the end of the year," said a Foreign Office spokesman on Tuesday.
The Government Communications Headquarters -- a giant, ring-shaped building nicknamed "the doughnut" -- is situated in the spa town of Cheltenham in southwest England.
It is at the heart of Britain's "special relationship" with the United States when it comes to spying, according to the documents.
They claim the NSA secretly funded GCHQ to the tune of £100 million ($160 million, 120 million euros) over the last three years.
One of Snowden's revelations was that Britain was running a secret Internet monitoring station in the Middle East, intercepting phone calls and online traffic, with the information processed and passed to GCHQ.
It also tapped into more than 200 fibre-optic telecommunications cables, including transatlantic ones, and was handling 600 million "telephone events" each day, according to Snowden.
"They are worse than the US," Snowden told The Guardian.
Called to appear before a parliamentary committee last November in response to the Snowden leaks, Lobban insisted the agency was not conducting mass snooping on the British public.
"We do not spend our time listening to the telephone calls or reading the e-mails of the majority," he said.
It was the first time a head of the agency had given evidence in public.
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