New Ucas statistics showed that 14,052 applications from Scotland were made by those wanting to embark on a degree course in 2013, down 3325 on levels recorded in 2010.
The figures also reveal an annual drop of 3.9% – or 565 fewer applications received this year compared to last.
However, the decrease in Scotland is nearly half that for the whole of the UK, which has seen a 5.6% drop in applications.
England, which has introduced fees, has seen a 6.5% decrease, with interest from potential students from Wales falling off at the greatest level – down 12%.
The figures also show a slight drop among other EU students, with applications down 1.9%. But the number of overseas students from outside the EU hoping to study at UK universities this autumn is up by 0.8%.
Ucas compares applicant numbers received at similar points in the application cycle, publishing the figures based on the picture available on December 17.
Of those received from Scotland, 12,769 were from first-time applicants, with the number of people reapplying dropping by 10%.
A spokeswoman for Universities Scotland said: "It's important to remember these figures are still a snapshot taken before all applications are submitted. Demand for university in Scotland remains very high, with the number of applicants still far outweighing the places available."