The University of St Andrews is the highest ranking in Scotland and is considered the third best in Britain, according to the Complete University Guide.
It is followed by the University of Edinburgh, then Glasgow, and finally Aberdeen.
But despite St Andrews, which counts Prince William and Kate Middleton among its alumni, topping the list for academic prowess, the principal earns nearly £100,000 less than her equivalent at the University of Edinburgh.
Principal of the University of Edinburgh, Peter Mathieson, earned £342,000 last year, after taking up the role in February 2018.
Last year lecturers represented by the University and College Union (UCU) went on strike for eight days between November and December, in protest at pensions, pay and working conditions.
And a spokesman for the UCU branded the hefty salaries pocketed by university bosses as 'out of touch' and 'an embarrassment to the sector', while it emerged this week that student loan debts have tripled.
Anton Muscatelli, principal of the University of Glasgow, earned the second highest in Scotland last year at £298,000 - a relatively modest £10,000 pay rise.
Despite being head of the country's most prestigious institution, the principal of St Andrews, Sally Mapstone was paid £260,000 last year - a pay rise of £11,000 from the £249,000 she earned between 2017 and 2018.
The top university said the 4.4 per cent pay rise awarded was 'very modest' in comparison with others in the sector.
Principal of the University of Aberdeen George Boyne earned £250,000 last year, data uncovered by student publication The Tab revealed.
Only 15 of the UK's top 42 highest paid vice chancellors and principals accepted wage cuts last year.
Public body the Scottish Funding Council refused to be drawn on the salaries but said universities 'make the best use of the resources available to them'.
The six-figure salaries were condemned by the Scottish branch of the National Union of Students (NUS), which described 'inflation-busting salaries' as 'extravagance'.
President of NUS Scotland, Liam McCabe, said: "It beggars' belief that some university principals continue to enjoy inflation busting salaries, benefits and bonuses while the public funding of our institutions continues to decline.
"Our universities are publicly funded charities, and should ensure transparency is a core principle of all decision making - giving the students and staff who make up our universities an insight into how that money is being spent.
"We cannot allow the extravagance of the few distract from the need from proper investment in our students.
"That means a fully funded sector, with the best educators, a wide variety of courses and classes, support services that are up to scratch, and financial support that meets the cost of living."
General secretary of the UCU, Jo Grady, said: "The largesse of vice-chancellors' pay and perks have been a continued source of embarrassment for the university sector and exposed how out of touch those at top of our institutions really are.
"At a time when staff pay has been held down, insecure contracts have become more common, pensions have been attacked and nothing done to address inequalities vice-chancellors continued to accept inflation-busting pay deals, max out expense accounts and enjoy rent-free accommodation.
"Staff have had enough and that is why they walked out on strike before Christmas, and are prepared to do so again if vice-chancellors continue to deny them fair pay and decent conditions."
A spokesman for the Scottish Funding Council said: "Universities are responsible for their own financial management and for decisions about their staff.
"However, we expect Scotland's colleges and universities to make the best use of the resources available to them."
A Scottish Government spokesman said: "As autonomous institutions, the salary levels of Principals and Vice-Chancellors are a matter for each university.
"However, we expect universities to exercise restraint in setting senior pay and that senior pay packages should be in step with the salary, terms and conditions offered to other university staff.
"Institutions must ensure the highest standards of transparency in setting pay awards."
A spokesman for the University of Glasgow said: "The Principal's salary is determined by a renumeration committee, which includes staff and student representation.
"He is not a member of that committee.
"Details of his salary are published on our website."
A University of St Andrews spokesman said: "Professor Mapstone's salary in 2019 was £260,000 per annum.
"Her salary rose from £249,000 in 2018, a rise of 4.4 per cent.
"St Andrews is consistently ranked one of the top three universities in the UK, but our Principal's salary is on the lower rungs of remuneration paid to UK Vice-Chancellors, substantially below the UK average of £350,000 and stands very modest comparison with others in the sector."
A spokesman for the University of Edinburgh said: "The Principal's salary is £342,000.
"There is no provision for any contractual lump sum payments of any kind.
"The salary was determined by the University's Remuneration Committee which consists of experienced independent members of the University's Court, our governing body.
"The Principal is not, and will not become, a member of Remuneration Committee.
"The Remuneration Committee took account of analysis of relevant UK and global benchmark data for Vice-Chancellors' pay in universities of similar size and complexity.
"It was judged that this level of salary was appropriate to attract the best candidate in an internationally competitive field and that it was commensurate with the size and scale of the responsibilities of the job."
A University of Aberdeen spokesman said: "Details of the Principal's salary are published on our website and in the University's Annual Report and Accounts.
"The Principal's salary and conditions of service are independently determined by the University's Remuneration Committee.
"The Principal is not a member of this committee."