The German giant’s supervisory board said they wanted a “new execution dynamic” in the top team as they announced he will be replaced by retail arm chief Christian Sewing.
Board chairman Paul Achleitner said that despite his “relatively short tenure”, Mr Cryan had played a “critical role”.
The outgoing chief will leave at the end of April, having been at the top of Deutsche Bank since July 2015, when he replaced co-chief executive Anshu Jain.
A month later Germany’s largest bank shook the financial world as it posted multibillion-euro losses due to a series of writedowns and litigation charges.
The six billion euro (£4.3 billion) hit led to a massive cost-slashing effort that saw the company cut thousands of jobs.
In the intervening years, Mr Cryan was promoted to sole chief executive and steered the bank through uncertainty surrounding Brexit, plummeting share prices, ultra-low interest rates and hefty fines from US regulators over the financial crisis.
Mr Achleitner said he had “laid the groundwork” for a rosier future, but added: “Following a comprehensive analysis, we came to the conclusion that we need a new execution dynamic in the leadership of our bank.”
A Deutsche Bank employee of more than 25 years, Mr Sewing, who is German, was promoted to “lead Deutsche Bank into a new era,” the chairman said.
“Christian Sewing has proven himself a strong and disciplined leader,” he said.
“The Supervisory Board is convinced that he and his team will be able to successfully lead Deutsche Bank into a new era.
“We trust in the great ability of this bank and its many talents.”
Most recently Mr Sewing was head of Deutsche Bank’s Private & Commercial Bank, having been head of group audit from June 2013 to February 2015.
With a background in risk, the new chief has worked for the bank in Frankfurt, Hamburg, London, Singapore, Tokyo and Toronto since joining in 1989.