Figures from admissions body Ucas, as of the January 15 deadline, reveal 14.7% more applications from England and 17.3% more from Northern Ireland, while 4.1% fewer people from Wales applied.
Total applications to Scottish universities to start courses this autumn, including from EU and non-EU countries, increased to 103,219, a rise of 7.1%.
The overall number of people in the UK applying to university is up almost 3% on last year, to 475,587.
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.
"These figures show Scots are already benefiting from our decision to ensure access to higher education is free and these students will also be some of the first to benefit from the best package of student support in the UK.
"I have already announced an extra 2,000 higher education places for next year, targeted at those progressing from college and students from deprived areas. I am confident that Scottish applicants will be able to achieve their goals of a university education and play their role in securing our economic future."
Alastair Sim, director of Universities Scotland, said: "Today's Ucas figures show that the offer of a quality Scottish higher education from Scotland's universities continues to be seen as an attractive and sound investment from students across the UK and internationally.
"As Scotland's universities look to deliver on their collective commitment to widening access we are pleased to see an increase in home applicants.
"We are also pleased to see students from the rest of the UK vote with their feet to apply to Scottish institutions, which have some of the best bursary and student support schemes in the UK to help with the cost of their study."