Most members of the UCU union, which represents lecturers and support staff, will be taking part in a two-hour walk-out.
Staff at the universities of Aberdeen, Robert Gordon and West of Scotland will strike for longer as their institutions will dock them a full day's pay regarless of how long they take action.
UCU said the universities would face a legal challenge to recover money it believes was unlawfully deducted.
The union is in a pay dispute with UK universities after they were offered a 1% pay rise, which they say will leave staff with a real-terms 13% pay cut since 2009.
The Universities and Colleges Employers Association, which negotiates on behalf of universities, argues it is the best deal available.