Women working at the Wellcome Trust earn 21 per cent less than men on average, according to a gender pay report issued by the charitable foundation.
The report shows that male employees are paid a median average of 20.8 per cent more than female employees, although this figure increases to 30 per cent when a mean average is calculated.
The gender pay gap at the Wellcome Trust is more than twice the national average. In the UK generally, women in full-time employment earn a median average of 9.1 per cent less than their male counterparts. The gap increases to a median of 18.1 per cent when part-time employees are included.
The report says that the gender pay gap at the charity exists mainly because of the disproportionate balance of men and women at different levels of the foundation. "Overall, around 64 per cent of Wellcome employees are women, but most of the highest-paid senior roles in Wellcome are held by men," the charity said.
The report says there is a mean gender bonus pay gap of 78.8 per cent in favour of men, although this falls to 6.5 per cent once its investments team is excluded from the figures.
The median gender bonus pay gap at the Wellcome Trust is 22.6 per cent.
The trust pays the highest salary in the sector, with a member of its investment team receiving £3.7m in the year to 30 September 2017.
The trust has also published figures showing the proportion of women employed at different levels of the organisation, with women outnumbering men at all levels of the company except for the upper quartile, which is 52.2 per cent male.
The charity said in a statement: "We have already begun working towards a balanced distribution of men and women throughout Wellcome. As we learn more about the specific barriers that disadvantage certain groups from progressing in our workplace, we will remove them.
"In November 2016, Wellcome made diversity and inclusion a priority area. To broaden the diversity of people we fund, engage with and employ, we need to change some of our internal structures and practices.
"Many of the priority area changes we’re committed to will also help to reduce – and eventually eradicate – our gender pay gap."
All public, private and third sector organisations with more than 250 employees in the UK are legally required to publish, by April, gender pay gap data on their own websites and on a government website.