The general secretary of the University and College Union received a pay and benefits package of more than £100,000 last year.
The union, which is in the midst of industrial action against higher education employers over pensions, pay and jobs, paid Sally Hunt a gross salary of £98,238 in 2009-10.
The UCU's annual return lists a total pay and benefits package of £126,502 for Ms Hunt, which includes employer's National Insurance contributions of £10,545, pension contributions of £15,555 and "car benefit" of £2,164.
Her gross salary rose by 0.66 per cent on 2008-09. Her total package of £126,502 represented a rise of 2.1 per cent.
But a UCU spokesman emphasised that this included NI and pension contributions, and said it would be "highly misleading" to characterise her gross salary rise as anything other than "modest".
The annual return lodged with the Certification Officer, which oversees trade unions' political funds and finances, also led to some confusion over the UCU's membership figures.
The return lists the union's total membership across further and higher education as 115,399. This would represent a 3.2 per cent fall on 2008-09 - a potential worry for the union as it prepared for industrial action.
But the UCU spokesman said that the figure was an error, adding that the union was grateful to Times Higher Education for drawing its attention to the mistake. He said membership stood at 121,539 in October 2010 and rose to 122,216 in February 2011.
The UCU returned a surplus of £535,748 in 2009-10. But Ms Hunt has warned that the union will be stretched financially by its five industrial action ballots across further and higher education.
In her report for the UCU's national executive committee meeting on 11 January, seen by THE, she says the ballots "will more than absorb all of the contributions to the fighting fund this year and the pressure on (the) higher education, further education and campaigns budgets and resource will be significant".
The union's spokesman said that "the fact we could absorb such large unforeseen costs stands as testament to the financial security of the union".
The return also sheds light on the UCU's property transactions. In November 2009, it exchanged contracts on the sale of its former headquarters in Britannia Street after buying a site in Carlow Street, both in central London. It funded the purchase by taking out a bridging loan to cover costs while the sale of the old building was completed.
However, the union has yet to complete this sale. In 2009-10, it paid £145,862 in interest on the bridging loan, with loan liabilities standing at £12.3 million.