York St John and Shropshire's Harper Adams have reported the worst gender pay gap of universities in England.
Women working at the two universities are paid 37.7% less than men, according to median average salaries.
Of the prestigious Russell Group universities, Durham fared worst with a 29.3% gap.
Across all universities in England, the average gender pay gap is 18.4% - meaning for every £1 men earn per hour, women earn 81.6p.
The Royal Central School of Speech and Drama in London was the only institution to pay women more than men - an average gap of 1.9%.
Agricultural university Harper Adams said its results were due to "historical issues of gender balance in certain employment sectors".
However, fellow rural specialist the Royal Agriculture University in Cirencester was one of only three universities to report a 0% pay gap.
What is the gender pay gap?
The gender pay gap is the difference between the median average hourly earnings for men and women.
It is not the same thing as equal pay. Equal pay has been a legal requirement for 47 years and means men and women doing the same job have to be paid the same.
There are numerous reasons why a company may have a gender pay gap. One might be if men occupy the majority of the top-paid jobs while women make up a larger share of lower paid jobs.
If all men and women working at a firm are put in two separate lines in order of salary, the median pay gap would be the difference in salary between the woman in the middle of her line and the man in the middle of his.
York St John said more than a fifth of its staff were paid student ambassadors - casual, low-paid staff, three-quarters of whom were women.
The University of Buckingham reported a 37% pay gap, the third worst.
The University of Warwick was second worst of the Russell Group - set up in 1994 to represent of some of the most prestigious names in higher education - with a gap of 23.4%, followed by Birmingham, at 23.3%.
Durham vice-chancellor Stuart Corbridge said the university recognised the gap was a "serious issue" and was "committed" to addressing it.
The University of Warwick said services such as accommodation, cleaning and support were handled in-house, and were skewing the figures as they were often low-paid roles taken on by women.
The University of Birmingham described its pay gap as an "ongoing challenge" but said it was "strongly committed to removing barriers to equality".
Of all higher education organisations in England, 124 of 133 reported their figures before Wednesday's deadline to publish gender pay gap figures.
Some or all of those which did not release figures may be below the 250-staff threshold.