Seamus McDaid replaces Bernard King, who finally retired as principal of the University of Abertay Dundee on 26 July after a long-running dispute with the institution’s court.
Professor McDaid takes up the post at an uncertain time for Scottish universities, which are facing a funding gap of at least £268 million compared with English institutions.
Universities north of the border are facing significant cuts to their funding, but Holyrood has said it will not plug the gap by putting up fees, as is happening in England in 2012.
Professor McDaid said the next few years would be “very challenging” but that he was confident about the sector’s future.
“We are very fortunate in Scotland that the public, parliament and government place such value on higher education and we take confidence from the robust assurances, given by government, to protect the quality of teaching and research in our universities,” he said.
Universities Scotland, the sector’s main representative body, said Professor McDaid, who already sits on its executive committee, leads the group’s work on efficiencies and is closely involved in the Funding Policy Group.
Professor McDaid started his career in accountancy but moved into academia, joining what is now Glasgow Caledonian University in 1976.
He was made principal of the University of Paisley in 2005, which became the University of the West of Scotland after merging with Bell College in 2007.
He said he was keen for Scottish universities to work more closely with schools, colleges and businesses.
Universities Scotland said he had a “strong international reputation” in public sector accounting and finance.
Alastair Sim, the group’s director, said: “I am delighted that Professor McDaid has stepped forward to undertake this service on behalf of Scotland’s universities at such a crucial time. He will be a positive and passionate voice for Universities Scotland.”