Gerhard Schindler, 63, will take early retirement from July 1, leaving the reins of the BND service to Bruno Kahl, a trained lawyer and currently high-ranking finance ministry official.
"The BND faces major challenges in coming years," said Peter Altmaier, chief of staff of Angela Merkel's chancellery, in a statement.
These "include the development of its profile given the changing security challenges" as well as the "organisational and legal consequences of the work of the NSA investigation committee," he added.
But German media speculated that the change was down to a combination of factors that included the BND's controversial cooperation with the NSA.
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An investigation committee said in a report seen by AFP in October that the NSA had handed lists of European government offices as targets for espionage to the BND, with the request for the results be sent back to the United States.
Although the report found that the BND whittled down the list of thousands of NSA targets over the years, it still maintained cooperation with Washington.
Kahl is a trusted aide of Finance Minister Wolfgang Schaeuble, and has been leading a ministry division in charge of privatisations, investments and federal real estate.