Union officials said they were angered by the institution’s refusal to rule out compulsory redundancies as it looks to reduce its headcount.
The university, which wants to cut its budget by ?10.5 million, is currently offering voluntary redundancy and early retirement packages.
Rachel Shanks, the UCU branch representative at Aberdeen, said members could not sit back and watch jobs disappear.
“Strike action is always a last resort, but unless the university rules out compulsory redundancies we feel we will be left with no other option,” she said.
“Aberdeen will only maintain its reputation for offering a student experience of the highest quality and excellence in teaching and research if the staff who undertake the research and teach the students are there to do the jobs in the first place.”
The strike ballot, which opened on 5 May and runs until 8 June, will also poll UCU members on their willingness to take action short of a strike, which could include only working contracted hours.
A university spokeswoman said Aberdeen’s voluntary redundancy scheme “aims to contribute to the long-term financial sustainability of the university and provide opportunities for us to invest in areas of strategic importance to us”, adding that the institution was “working tirelessly to consider other options to contribute to the savings that are required”.
“We are extremely disappointed to learn that in the midst of ongoing dialogue the UCU has decided to ballot its members for strike action and action short of a strike,” the spokeswoman said. “Our efforts are strongly directed at achieving our savings target through voluntary measures and the opportunity is open for a further two months.
“Almost 30 per cent of academic staff are members of the UCU and we would hope that staff generally will consider this as a time for partnership and team-working rather than confrontation.”
The ballot was launched as staff at the University of Dundee went on strike for a second time on 5 May, also in protest at the threat of compulsory redundancies.
Employees at Dundee, which is looking to axe about 85 roles, had previously walked out on 28 April.