Mr Pilling, a former First Direct CEO, said he had decided to step down in order to pursue new opportunities that will allow his to spend more time with his family.
Chairman John Heaps said his decision to step down was a personal one.
Mr Pilling said: “After nearly five years as chief executive of the society during a period of significant change, I have decided to step down with the intention of pursuing new and different opportunities that will give me more balance with my family life.
“From a personal perspective, I believe now is the right time for me to do this and for the board to appoint a new chief executive to continue to take the society forward.
“The society is in a strong position despite the challenging markets and it has been a privilege to have been part of its recent history and success. In the meantime, it is business as usual.”
Chairman John Heaps said: “It is with regret that I have to announce that our chief executive Chris Pilling intends to step down. This is entirely a personal decision on Chris’ part. I would like to thank Chris for his tremendous contribution to the continuing success of the society over the past five years.
“Chris has provided outstanding and strong leadership and demonstrated a deep commitment to ensuring that our members’ interests are at the centre of everything that we do. He has developed an excellent management team and they remain clearly focused on continuing to manage the society.“
Yorkshire said that the process of finding a suitable successor to build on Mr Pilling’s achievements has already started.
In the meantime, Mr Pilling will remain chief executive and continue to work with the rest of the board.
Mr Pilling received the biggest pay package out of Yorkshire’s top three building societies last year at £918,000.
Yorkshire is the UK’s second biggest building society after Nationwide. Skipton is Britain’s fourth biggest building society and Leeds is the fifth largest.
Mr Pilling’s total remuneration included a salary of £571,000, a pension contribution of £92,000, variable pay for in-year performance of £71,000 and deferred variable pay from previous years of £169,000. He earned a total of £923,000 in 2014.
Yorkshire reported an 8 per cent fall in pre-tax profits in 2015 as competition intensified in the mortgage and savings markets.
The society said that it achieved a strong financial performance in 2015, with a record core operating profit of £185m, compared with £179m the year before. Pre-tax profit fell to £173m, which is down from the £188m reported in 2014.
Mr Pilling said the group had achieved a strong set of results in a challenging and competitive year in the financial services industry.
“Interest rates have remained at historically low levels for mortgages and savings customers and competition within the market has become even more intense,” he said.
“As a result, during the year we proactively reduced our lending and funding targets to reflect our commitment to long-term financial sustainability whilst continuing to offer extremely attractive mortgage and savings products.”
He said this including launching the society’s lowest ever fixed rate mortgage.
Yorkshire is in the process of rebranding its Chelsea and Barnsley branches and is closing 22 branches as part of an overhaul. It said the closures largely fall where branches are less than a mile apart.
Mr Pilling said he did not expect the environment to become any less intense this year.