The St Cuthbert Window is one of the largest survivors of its type in the world and is almost 600 years old.
All 152 panels of stained glass in the window will be individually removed by experts from the York Glaziers Trust alongside work to the stonework of the surrounding transept.
The Minster's own team of stonemasons will then carry our urgent repairs on eroding and decaying masonry.
Each panel will be cleaned and repaired by conservators and a number of them will be included in an exhibition called Light, Glass & Stone which will run during the five-year restoration.
The window itself tells the story of the Anglo-Saxon monk and Bishop of Lindisfarne who was later sanctified as St Cuthbert. It has not undergone any major conservation work since the 1940s.
York Minster's director of works Alex McCallion said: “The St Cuthbert Window is one of the three great windows in the Minster’s East End alongside the St William and Great East Windows, both of which have undergone major conservation and restoration projects in the last two decades.
“Now, after centuries of exposure to the elements, the stonework of the window and South East Transept in which it sits has eroded and decayed in places and needs urgent attention.
“The removal of the stained glass will allow a thorough inspection of the masonry to be undertaken, before we start the programme of stonework which includes dismantling and rebuilding two huge supporting buttresses, repairs to the window’s tracery and the carving of new grotesques.”
York Glaziers Trust director Professor Sarah Brown added: “The window dates from around 1440 and is a rare surviving example of a medieval narrative window, telling the story of St Cuthbert’s life on a monumental scale.
“The essential repair of the stone of the South East Transept has created a once in a lifetime opportunity to conserve the window, which was last restored following the Second World War.
“The team’s work will include intricate cleaning and repairs to the glass and the lead matrix before it is returned to the window with state-of-the-art protective glazing. This will replace external quarry glazing installed in the 1930s and provide a barrier between the medieval glass and the elements to ensure its survival for generations to come.”
The accompanying exhibition will open in June and run until 2024.