But applicant numbers have not recovered to the levels of 2011, the year before tuition fees were tripled for students from the rest of the UK, now sitting at a maximum £9,000 a year. Compared with 2011, applications are down 6.1%.
People in Scotland who take up a course north of the border do not have to pay tuition fees.
The number of Scottish students applying to study in Scotland rose from 38,559 last year to 39,358 this year, an increase of 2.1% (190 more applications).
An analysis of the figures also revealed that 18-year-olds from the most disadvantaged areas of Scotland are around 80% more likely to apply than they were in 2004.
Education Secretary Mike Russell said: "It is good news that a record number of people living in Scotland have applied to university next year and that our universities continue to be a coveted choice around the globe. I am particularly pleased to see more school leavers from deprived areas applying."