A study by the Scottish Funding Council examining the careers of students who left university in 1999 shows the average pay of female graduates was 22,700 by 2002-3. By sharp contrast, male graduates were earning 25,800 on average - or 3,100 more.
In particular, male graduates in law, mathematics, computing, medicine and engineering all enjoyed "considerably higher earnings" than their female peers, the study found.
Although the report, Scotland's Class of '99, stresses that the gender pay gap in Scotland is 800 narrower than south of the Border, it says it remains a major problem in the workplace. It states: "While it is a positive result to find that the gender pay gap is, in general, lower for graduates from Scottish higher education institutions (HEIs), it is important not to lose track of the fact that the pay gap still persists.
"However, more detailed analysis of the male and female graduates from Scottish HEIs identifies considerable variation in the size and direction of the pay gap."
The report also found that while the gender pay gap among graduates was evident across all sectors, it was most prevalent in the agriculture, mining and quarrying sector, the construction sector, the transport and tourism sector and the banking, finance and insurance sector.
Robin McAlpine, spokesman for the higher education umbrella group Universities Scotland, said a person's gender should have no bearing on their earning capacity.
He said: "Universities prepare people for the workplace to the same quality irrespective of their gender, race or anything else. We hope we see the day soon where the labour market can see that the graduates we produce are of the same value, irrespective of things like gender.
"We can all do more to encourage people to think about education and careers in a less gender stereotyped way. We still don't get enough women into science and technology courses and these can offer very interesting and lucrative careers. There is no justification for the pay gap on educational terms."
Two weeks ago, a separate study by the Higher Education Statistics Agency found that male graduates can expect to earn up to 4,000 more per year in their first job than their female counterparts.
And earlier this year, a report by the Women in Work Commission revealed that a 17 per cent pay gap between men and women still existed in full-time work, despite the passage of gender equality laws 30 years ago.
A spokeswoman for the Fawcett Society, a charity that campaigns for gender equality, said: "The pay gap, especially for part-time work, has proved very stubborn.
"Thirty years after the introduction of equal-pay legislation, it's a scandal that the gap still exists."
The spokeswoman added: "We need more enforcement of the rules and more workplace flexibility from employers."
The study also reveals that 83 per cent of graduates from Scottish universities had secured graduate-level employment within four years.
Some 96 per cent of those who took part in the research also said that they enjoyed their time at university and would enter higher education again if they were given the choice.
Scots graduates were also less likely to be in debt than their English and Welsh peers, although a significant minority said debt had deterred them from further study.
Roger McClure, the chief executive of the funding council, said: "This survey strongly indicates that getting a degree is worthwhile both for individuals and the economy."
Janet Lowe, the chair of the funding council's skills committee, added: "This is the latest survey to show that not only are graduates satisfied with their higher education experience, but they are also achieving positive outcomes in the labour market."