Announcing his intention to retire, Mr Clyne said the chief executive role was the most rewarding of his career but has also taken a "personal toll".
Mr Clyne said he is proud to leave NAB as a strong, customer-focused bank.
“We have built a strong foundation for future growth with the revitalisation of the Personal Bank; grown our already strong position in business banking; and achieved material improvements in customer satisfaction and reputation," he said.
"We have also worked methodically through our legacy issues while still making transformational change in our technology."
NAB chairman Michael Chaney said NAB's new chief executive, Andrew Thorburn, was an "outstanding banking executive who has been part of the NAB Group executive team that developed the bank’s successful strategy focusing on building a stronger Australian and NZ franchise".
"Andrew Thorburn has done a superb job leading Bank of New Zealand since 2008 where he continued to build the bank’s performance, increasing cash earnings by more than 40 per cent, improving market share on the back of strong customer satisfaction and developing a strong leadership culture," Mr Chaney said.
A replacement for Mr Thorburn at Bank of New Zealand will be announced "in due course", a NAB statement said.