The £36m project, which forms part of the Scottish Government's £1.25bn Scotland's Schools for the Future building programme, will facilitate more than 1,000 pupils when it opens in 2015.
The new building is receiving £25m directly from the Scottish Government.
Welcoming the commencement of site works, Minister for Learning Alasdair Allan said: "Ellon Academy is a large rural, comprehensive secondary school with a long tradition of excellence and a strong relationship with the local community.
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"Today marks an exciting development for both the school, its pupils and the wider community – by 2015 the school building will have been replaced with a state of the art facility aimed at providing pupils with the best possible environment for learning.
"This is one of 67 schools being replaced or refurbished as part of the £1.25 billion Scotland's Schools for the Future programme, and one of three in Aberdeenshire – work at Mearns Academy is already underway and I expect to see progress at Alford Academy by the spring.
"By the time the Programme finishes the Scottish Government, together with local authorities, will have lifted over 46,000 pupils into top quality accommodation, helping ensure that our children and young people have the best possible chance of being ready for the global jobs market."
(JP/MH)
