The decision by St Andrews University means students will pay £36,000 for a four-year degree. By comparison, the cost of a degree at Oxford and Cambridge, regarded as the best in the world, will be £25,000 from next year.
Earlier this week, Edinburgh University became the first in Scotland to announce plans for a £36,000 degree.
Edinburgh’s Heriot-Watt and Aberdeen also announced fees of £9000 a year, although the total cost of a degree will be capped at £27,000.
The news comes just weeks after Education Secretary Michael Russell said he expected Scottish universities to show restraint in setting fees, with £6375 a year quoted as a competitive figure.
Last night, St Andrews officials said new bursaries introduced alongside higher fees would alleviate the burden for poorer students from the rest of the UK, and said the £9000 fee was not even enough to cover the cost of teaching, which they said was £11,772 a year.
University principal Louise Richardson said: “A fee of £9000 per annum to attend St Andrews is a good deal and does not cover the cost of the education provided.”
But Patrick O’Hare of the Student Association said: “This unprecedented hike is precisely the wrong message to send out when St Andrews struggles to attract students from state schools.”
l St Andrews was named best university in Scotland in the Sunday Times University Guide 2012. Glasgow climbed to second, with Edinburgh in third. Heriot-Watt University in Edinburgh was named as Scottish University of the Year, while Robert Gordon University in Aberdeen was named top modern university.