The tree which is present on the very first Ordnance Survey map, created in 1866, will now be chopped down to make way for a sports pitch at Perth Academy.
Staff, pupils and parents had fought to save the tree but received the news they had been dreading from the rector of the school. Jonathan Lothian said attempts to redraw a sports pitch plan to accommodate the tree had been unsuccessful and Perth & Kinross councillors had decided to go ahead with the original plan.
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On the school's website he posted a message which said: "I realise that this may be disappointing news for some in terms of the removal of the tree.
"However, I am sure you will appreciate the reasons why this project should proceed and that the community of Perth Academy will benefit in the longer term from the provision of an all-weather pitch.
The campaign had an added poignancy as the tree had come to be regarded as a memorial to Callum and Ethan Owen, who died in 2009 in a road accident that also claimed the life of their mother, Michelle.
A commemorative bench at the foot of the tree will now be relocated after talks with the Owen family, said Mr Lothian.
Andrew Fairbairn, from the Woodland Trust Scotland, said: "This decision calls Perthshire's reputation as the 'Big Tree Country' into question. I am dismayed that the views of the parent council, pupils and staff have been ignored, the council has ridden roughshod over them."