The Universities and Colleges Union, which represents lecturers, announced the ballot after what it described as a "miserly" pay offer of 1%.
The union said its members at universities across the UK had not received a "meaningful" pay increase since October 2008, with four consecutive years of cuts amounting to 13% in real terms.
As part of its pay claim, the union also called on the employers' association that negotiates on behalf of UK universities to address other issues such as leave, the gender pay gap, increased workloads and the increasing use of zero-hour contracts.
Mary Senior, the union's Scottish official, said: "What is very clear is that the employers can afford to pay their staff more than the miserly 1% that is on offer, but they are making a calculated choice not to.
"Those in charge of universities continue to drive down terms and conditions and pay for the majority of staff.
"At a time when staff have been under greater pressure to develop research portfolios and deliver widening access initiatives for more students, they are having to cope with increasing workloads and they have they pay held down".
However, the Universities and Colleges Employers Association said the 1% offer and joint work around the other issues raised by the union was a "sustainable offer".
A spokesman said: "The current UK-wide circumstances remain unchanged, with higher education institutions continuing to operate in challenging and uncertain environments.
"Institutions are also now in a regime of funding their own infrastructure investment, so suggestions that any surpluses be devoted to pay are misguided."
The union's ballot will open next Wednesday and close on October 10. A yes vote could result in industrial action during the autumn term.