The Educational Institute of Scotland (EIS) has published figures showing the reserves of higher education institutions rose to £2.9 billion last year.
In addition, the sector made an overall operating surplus of £90 million in 2012/13 - while total income rose by 6.4% to £3bn.
EIS lecturer members in Scotland will join their higher education colleagues across the UK in strike action tomorrow in protest over pay.
Larry Flanagan, general secretary of the EIS, said: "This report is a substantial piece of work that lays bare the healthy financial position of higher education institutions in Scotland.
"At a time when lecturers are fighting for a fair pay rise, after years of pay restraint and declining real-term salaries, it is quite shocking to see evidence of the very healthy financial position of our universities - mostly built on public money."
However, a spokeswoman for Universities Scotland, which represents university principals, criticised the EIS for using university reserve figures to negotiate a higher pay settlement. She said: "Reserves are the value of all university assets - it is not cash and it cannot be easily used to fund pay. The EIS also neglects to mention that, in the last five years, the staff wage bill in Scotland has increased by over £138 million and it is right the employers' negotiating body is looking to manage these costs.
"It is, in our view, highly counterproductive for the unions to wilfully paint a misleading picture of universities' financial condition."