[1][2][3] On 16 July 2021, Archbishop Virgílio do Carmo da Silva, submitted an application to the Ministry of Higher Education, Science and Culture to establish a university.

[1][2][4] The new university, the archbishop said, would incorporate and expand upon the diocese's existing higher education institution, the Instituto de Ciências Religiosas (ICR).

[1][2][4][5] A month later, on 13 August, da Silva met with Prime Minister Taur Matan Ruak to discuss the process, after which the archbishop said he hoped the university could open later that year.

[6] The Universidade Católica Timorense São João Paulo II was inaugurated on 8 December by the archbishop and Prime Minister Taur Matan Ruak at its campus in Dili's Balide neighborhood.

[3][5][7][8][9] The university, Archbishop da Silva said, would "provide a world-class education in all areas of human activity, inspired by the Catholic intellectual, moral, and spiritual traditions.

"[3][7][9] On 14 December, Archbishop da Silva inaugurated UCT's first rector, the Franciscan friar Joel Casimiro Pinto, other administrative officers, and the 31 members of the university council.

[3][5][7] UCT opened its academic year on 24 March 2022 with a ceremony attended by Archbishop da Silva, former president José Ramos-Horta, and Holy See representative Msgr.

[11] The university awarded degrees to 31 graduates from the faculties of education and social sciences, including students who previously attended the stand-alone Instituto de Ciências Religiosas.

[4][12] On 22 October 2023—the feast day of St. John Paul II, the university's patron saint—UCT held a mass, led by Archbishop da Silva, to commemorate UCT's first anniversary and lay the foundation stone for a new four-story building on campus.

[14] Donors to the library's collection included Prime Minister Xanana Gusmão, politician Paulo Remédios, and Ramos-Horta, who alone contributed 3,400 books.

[13] The building is being constructed by an Iranian company and financed by the archdiocese using funding provided annually to the church by the government for educational, social, and administrative purposes.

[16] The rector is assisted by a general administrator and four vice-rectors: of institutional and pastoral development; of postgraduate studies, research, and cooperation; of teaching and academic affairs; and of student support.

[18] On 9–10 July 2024, ANAAA representatives visited UCT to conduct an initial evaluation, which resulted in a provisional report and recommendations for the university to implement to receive accreditation.