If an athlete goes through any part of male puberty, they will not be allowed to compete in elite races.
The policy requires trans competitors to complete their transition by the age of 12 in order to compete.
An 'open' category will be established for swimmers who have a different gender identity than their birth sex.
The policy was passed with a large majority of votes.
The congress was held at the World Championships in Hungary.
A report from a task force made up of leading figures from the world of medicine, law and sport was heard by members of the financial community.
The UCI doubled the period of time before a rider transitioning from male to female can compete in women's races.
The issue in swimming has been brought to the attention of the public by the experiences of American Lia Thomas.
In March, Thomas became the first known trans swimmer to win a US college swimming title.
Thomas started hormone replacement therapy in the spring of 2019.
She broke records for her swimming team.
More than 300 college, Team USA and Olympic swimmers signed an open letter in support of Thomas, but other athletes and organizations have concerns about trans inclusion.
Some of Thomas' team-mates and their parents wrote letters in support of her right to transition, but said it was unfair for her to compete as a female.
In February of this year, USA Swimming updated its policy for elite swimmers to allow trans athletes to swim in elite events, as well as reduce any unfair advantage, including testosterone tests for 36 months before the competition.
There's more to come.