The Financial Conduct Authority, which regulates the country's biggest firms, has revealed it pays its male staff a fifth more than its female staff.
The watchdog's median gender pay gap was 21.2% in 2018 - up from 20.9% in 2017 despite a pledge to improve.
The average gap across all UK companies last year was half the size at 9.7%.
Nicky Morgan MP, Chair of the Treasury Committee, said the FCA's pay gap was going in the "wrong direction".
It comes as campaigners and MPs are calling on the financial services industry to tackle its large gender pay disparities.
Andrew Bailey, the head of the City watchdog, has also repeatedly called for a cultural overhaul in Britain's finance industry, saying that a lack of diversity in the workplace can create "groupthink".
The figures, which were first released in November but not widely reported on at the time, show much of the gap was due to an imbalance of women in senior leadership roles.
Some 61% of workers in the top quartile of pay at the FCA were men versus 39% who were women.
The big employers with the highest pay gaps in 2017:
- Barclays Bank PLC: 43.5%
- Lloyds Bank: 42.7%
- Aberdeen Asset Managers: 37%
That fell to 56% who were men in the middle quartile and 43% in the lower quartile.
The agency said a greater proportion of women were paid bonuses than men in 2018, although the bonuses for women were 25% lower.
However, it did increase the number of women and black and ethnic minority staff in its senior leadership team.
"The FCA's gap is below that for most firms we regulate but this does not make us complacent and we are committed to reducing it," a spokeswoman said.
All UK companies with more than 250 employees are expected to publish their gender pay gap by 4 April as well as demonstrate what progress has been made since April 2018.
Only around 750 have done so already leaving about 10,000 who are still to report.
Last year more than half of the companies that reported did so in the week before the deadline, while around 1,500 missed the deadline.
Of the larger companies to have reported already, Lloyds Bank, Smiths Medical International and HSBC are the worst offenders with pay gaps of 41.7%, 36.7% and 31% respectively.
Sam Smethers, head of the Fawcett Society, which campaigns on gender equality issues, said: "The Financial Conduct Authority is like the majority of other public bodies, it has a gender pay gap. What matters is what they are doing to tackle it.
"The financial services sector has one of the largest gender pay gaps. Women are repeatedly under-represented in senior roles and a macho culture holds women back."