Its creation in 1875 was initiated by lay Catholics following passage of a law on the freedom of higher education.
Since 2005, the Catholic University of Lyon has been located on two campuses that are close to each other in the city center: UCLy is now situated on three campuses, two within the heart of the city of Lyon (Carnot / Saint Paul) and the other, in Annecy, which opened at the start of the 2020 academic year.
UCLy is a non-profit-making organisation granted the status of a public interest private higher education institution (EESPIG) by the French government, and as such, it contributes to providing the public service of higher education.
The rector since September 2024 is the theologian Grégory Woimbée.
The university offers a government-backed diploma in religious freedom and secularism, designed especially for foreign Muslim imams; however, not enough people enroll in it.