The high street mutual said the plan will "support an orderly transition to new leadership" in what will mark a clean sweep at the top as chairman David Roberts also heads for the exit.
Kevin Parry - Royal London Mutual Insurance Society chairman - has been appointed as deputy chairman and chairman elect. He is set to replace Roberts by March next year.
As chairman elect, Parry, who is Nationwide’s current senior independent director,will lead the process to appoint a successor to CEO Garner.
Roberts said: "Joe has made an outstanding contribution as leader of Nationwide. He has led the society through the challenges of Brexit and Covid, and we have emerged in robust financial health able to focus on supporting our members as the country rebuilds from the effects of the pandemic.
“Over the last six years, the growth in our membership, mortgage lending and deposits aligned with our consistently superior customer service is testament to Joe's focus on delivering the things that are important to our members.
"By putting in place an orderly transition, we will ensure a smooth handover to new leadership and continuity in the running of the society."
Garner said: "The foundations we've laid down in recent years will enable my successor to continue to grow the society and ensure we are ready to meet the future needs of our members.
"Until that point, I am absolutely focused on continuing to lead and deliver on our priorities."
Parry added: “Nationwide Building Society has been part of the UK's economic and social fabric for over 150 years, and I'm honoured to be given the opportunity to help shape its future.”
The society, which rescued the Dunfermline Building Society during the financial crisis, confirmed that Garner would remain in post until a successor is appointed and is not leaving for another role. It will lead an internal and external search.
Garner took the top job in April 2016, joining from BT Group, where he had been chief executive of Openreach since early 2014. He was also previously head of HSBC in the UK.
Roberts, who has been chairman of Nationwide since 2015, asked the board earlier this year to start planning for his successor.
Releasing its annual report in May, the society revealed that deposits during the past year had increased by a bumper £10.6 billion, which compared with £5.7bn during the year before the pandemic struck.
The lender added that those who struggled financially during the pandemic were helped with 256,000 mortgage payment holidays and 105,000 payment breaks for loans and credit cards.
The details come as the group revealed pre-tax profits in the year to April 4 nearly doubled from £466 million to £823m due to a rise in income and cost-cutting measures across the business.
Mortgages remained strong, with customers taking advantage of the stamp duty holiday.