In a further escalation of its industrial action, the University and College Union (UCU) said it had given the go-ahead for its members to refuse to mark exam papers and assessments if the dispute was not resolved in the next two months.
The move, described by the union as its "ultimate sanction", could mean that students are left without the final results they need to gain their degree, and therefore would be unable to graduate.
The dispute focuses on a 1% pay rise offered to university staff, which UCU insists means that their members have faced a 13% pay cut in real terms since October 2008.
UCU, along with a number of other unions, has already staged three one-day national walkouts as part of its campaign, and has also held a series of two-hour strikes aimed at disrupting teaching.
University employers have previously expressed disappointment at the action, and maintained that the strikes were not well-supported.
UCU said its marking boycott - which would be the first to be conducted by the union since 2006 - will begin on April 28 if a pay deal is not reached.
The union said it hoped that employers would sit down with them to work out a pay settlement in the next few weeks, adding it had been frustrated with employers' stance on the issue.
UCU Scotland official Mary Senior said: "A marking boycott is the ultimate sanction, but an avoidable one if the employers will negotiate with us over pay. No-one wants to see this dispute escalate, but in the continued absence of meaningful negotiations from the employers, we are left with no alternative.
"I fail to see how any university can claim to have students' best interests at heart if it is not pushing for talks with the union to resolve this dispute.
"Even now the timetable we have set provides a generous window of opportunity for the employers to address our just demands, which we hope they take."
She said the support for action so far demonstrated how angry staff were at the "hypocrisy" over pay at universities.
She added: "The employers cannot plead poverty when it comes to staff pay and then award enormous rises to a handful at the top."
However, UCEA, the body that negotiates on behalf of universities, said the threat of a boycott was disappointing because it was directed at students.
A spokesman said: "Both UCU and higher education institutions are well aware that strike support has dwindled still further in recent weeks, with the overwhelming majority of staff not taking part and having no wish to disrupt students' education.
"It is quite extraordinary for the UCU to be planning yet more action over last year's pay uplifts with the 2014/15 pay negotiations due to start in March, a full month prior to the start of their threatened marking boycott."
The spokesman said last year's pay increases, averaging 3%, had already been paid.
The organisation also warned that institutions would continue to dock pay for staff taking part in industrial action.
The pay increases in 2013/14 comprised of a nationally negotiated rise of 1%, with individual increments and merit awards costing institutions around 3%.