The Educational Institute of Scotland (EIS) said its 1500 members would take part in a one-day strike later this month as part of a wider programme of action.
The walkout will particularly impact on Scotland's newer universities, where EIS membership is stronger.
A similar ballot by UCU Scotland union, which has 6000 members, rejected strike action, although members backed action short of strike action, which could include a work to contract.
The dispute centres on an offer of a 1% pay rise for 2012/13 to university staff from the Universities and Colleges Employers Association (UCEA).
The offer is in response to a 7% pay claim by unions including an increase of 3.7% to keep salaries in line with inflation and a further rise of 3.3% to catch up with real terms pay cuts over the past three years.
UCEA, which negotiates on behalf of UK universities, believes the pay offer is the best available at a time of tight funding for institutions. However, unions argue the last public funding settlement from the Scottish Government was large enough to allow for an improved pay offer.
Unions representing university support workers are also balloting over the same pay offer.