The report, which looks at salary and labour turnover rates for 2577 people, revealed the average male in an executive role in Scotland earned a basic salary of £40,118 over the 12 months to August 2012, compared to £29,480 for a female in the same type of role.
The difference in executives' salaries north of the Border is higher than the UK average of £10,060 a year and is the second biggest pay gap after London.
The National Management Salary Survey is published by XpertHR in association with the Chartered Management Institute (CMI).
Previous studies have highlighted stark gender imbalances in the boardrooms of major Scottish companies, although recent figures have pointed to some improvements.
Ian Andrew, of CMI Scotland said: "Businesses have been focused on getting more women on boards, but we've got a lot to do on equal pay and equal representation in top executive roles.
"Women make up almost three out of four at the bottom of the ladder, but only one out of four at the top. This lack of a strong talent pipeline has to change and fast. Allowing these types of gender inequalities to continue is precisely the kind of bad management we need to stamp out. Companies are missing out on the full range of management potential when we need to be doing everything we can to boost economic growth."
The Herald revealed in June that the number of women serving in the boardrooms of Scotland's leading 30 listed companies had risen from 29 to 37 in the previous 12 months.
However, nearly 85% of directorships are filled by men. Eight companies are overseen by an entirely male board, down from 10 a year ago.
At a UK-wide level, although female junior executives earned marginally more – £363 – than males at junior levels for the second year running, the gender pay gap remained substantial at the opposite end of the executive career ladder, with female directors typically earning £14,689 less than the male director average of £141,946.
The figures show that while 69% of junior level executives are now female, a much smaller percentage have made it into top roles – just 40% of department heads are female and only one in four are chief executives.
The labour turnover data at a national level also shows more women than men fell foul of job cuts between August 2011 and August 2012, with 4.3% of female executives made redundant compared to 3.2% of male bosses. This difference grows as women move up the ranks, with twice as many female directors made redundant compared to males.
Mr Andrew said: "The Government should demand more transparency from companies on pay, naming and shaming organisations that perpetuate inequality and celebrating those that achieve gender equality in the executive suite.
"Plans to require companies to report on the number of women in senior positions are also welcome.
"The Government should move ahead with plans to reform parental leave, which will remove one of the barriers that makes it impractical for women to play a greater a part in the workforce."
l The pay and jobs prospects of women are going into reverse because of Coalition austerity measures, the Fawcett Society has warned.
The campaign group said today marked the point in the year when women in effect started working for nothing because of the gender pay gap.
It said women will be hit by plans for regional pay in the public sector and proposals to swap employment rights for shares in a company.