Statistics from the Scottish Funding Council (SFC) show an increase in the number of students undertaking first degree and postgraduate research courses.
In total, 96,975 students began studies at universities in 2012/13, up from 95,350 in 2011/12, but down on a high of 108,840 in 2009/10.
The number of entrants to first degree study increased by 4% to 46,870.
Meanwhile, the number of higher education qualifiers - those who have passed their course - in 2012/2013 increased by 2.9% from the previous year to a record 95,580, with 36,050 of these students gaining a first degree.
Minister for Learning Alasdair Allan said: "Today's figures bring a range of promising news for Scottish higher education. A record number of qualifiers provides further evidence of excellence at Scottish institutions, enhancing our global reputation still further.
"These figures also follow the confirmation this week that Scotland is the only country in the UK to have increased its funding for higher education in the last year, with investment now exceeding £1 billion."
The statistics also show that the number of higher education entrants from the most deprived areas increased to 15.8%.
"A record level of entrants from the most deprived areas of Scotland also reflects well on our efforts to widen access, and is something I expect to see more of as we reap the benefits of the Post 16 Education (Scotland) Act," Mr Allan said.
"What we now have is a very bright picture for the future. New entrants have increased and the latest Ucas figures show that the number of Scots-domiciled applicants are up, demonstrating resilience in the wake of sizeable tuition fees elsewhere."