Professor Ian Diamond, principal of Aberdeen University was knighted for services to social science and higher education.
And Professor Pamela Gillies, principal of Glasgow Caledonian University, was made a CBE for services to education and public health.
Meanwhile, Professor Peter Ware Higgs, Emeritus Professor of Theoretical Physics at Edinburgh University was awarded the Companion of Honour for services to physics.
Ms Gillies said: "I feel extremely honoured to be recognised in this way, but of course this award reflects the combined efforts of the many colleagues I have worked with over the years.
"I am especially proud of the social impact and benefit of the work of the staff and students at Glasgow Caledonian University. It is a privilege to be principal of such a fine university."
A native of Dundee, Ms Gillies graduated from Aberdeen University with a BSc in Physiology before taking a Masters in Education and Philosophy and training as a teacher.
She has long worked tirelessly towards improving public health through research and education and has researched and written widely on HIV/Aids, health development, and inequalities in health, focusing on the potential of social action for health improvement.
This work has taken her to Geneva where she contributed to the World Health Organisation's Global Programme on Aids, to Harvard in the US where she served as a professor in health and human rights and to India and Brazil.
Since joining Glasgow Caledonian, Ms Gillies has also championed social change through her support for common good initiatives including the work of the Caledonian Club, which promotes widening access to university education.
Meanwhile, Moira McArthur, the headteacher of Sandaig Primary School in Glasgow, is to receive an MBE for services to education and the community in Glasgow.
Local councillor Stephen Curran, executive member for education and young people, said: "This is a well deserved honour for an extraordinary person."