"We don't actually go out of our way to look for external recognition, but it's very nice when you receive it," said an excited college principal David Shepherd.

Mr Shepherd said the award was recognition for the hard work of the entire college community including staff, students and parents.

At a virtual awards ceremony for the Australian Education Awards on Thursday night, Ballarat Clarendon College beat Toorak College in Mount Eliza, and Brisbane's Ormiston College and St Paul's School, for the non-government school title.

Clarendon Junior School also received an excellence award in the Australian Primary School of the Year (non-government).

"Staff have worked very hard with parents and children, and in particular this year has been a great challenge for everybody so it's really nice when the fruits of their labour are recognised," Mr Shepherd said.

The judges cited Clarendon's high VCE and NAPLAN scores, and student progress among the reasons for awarding the school the top honour.

The judges also wrote: 'Impressive application, the school has a strong professional learning program, impressive VCE results and a broad extra-curricular program'; 'Great structures to support quality evidence based teaching and learning'; 'Students have achieved above average gain over past 6 years'.

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After last year's VCE results the school was ranked Victoria's top performer based on a combination of its median VCE study score and the percentage of study scores of 40 or more.

"It is humbling to be acknowledged - again - by our peers in the education community that we're delivering on our commitments to our students and their families," Mr Shepherd said.