It was founded in July 1960 by the Society of Jesus on land donated by the Somoza family and was the first private university in Central America.

On August 16, 2023, through a spurious judicial decree, the university was closed and confiscated by the government of Daniel Ortega, accusing it of operating as a center for "terrorism" by organizing "delinquent groups," within the framework of the political crisis that Nicaragua has been experiencing since 2018 following protests against reforms to the Nicaraguan Social Security Institute.

Centro Superior de Idiomas (CSI) at UCA offers a variety of programs open to all who are interested in studying languages: English (for children, adolescents, and adults as well as ESL),[4] German, French, Japanese,[5]) Russian, and Spanish for foreigners.

[6] Center for Molecular Biology (CBM) was established at the Faculty of Science and Technology at UCA in 1999 with financial help from the Pew Foundation, New England Biolabs, WHO, and the University of California San Francisco.

As the first molecular research center in Nicaragua it addresses human, economic, and industrial development as well as environmental, agricultural, and health issues.

It organizes the National Biotechnology Congress which includes Nobel Prize winners among its participants, and helps shape public policy.

[12] The University assists students and alumni to make contact with private and public institutions for both temporary internships and more permanent placement.

[16][17] Spiritual Exercises of St. Ignatius of Loyola, an ordered sequence of meditations and contemplations fostering a greater awareness of God in one's life.

Thus began the experimental radio station for students of journalism to get pre-professional practice, with support from the Deputy Minister of Telecommunications (TELCOR) Bayardo Altamirano.

In the succeeding years the most active reporters took over as directors of the station: Gustavo Adolfo Montalvan, Alina Guerrero, Luis Lopez Ruiz, and Azucena Castillo.

In 2017 recent reports covered the topics of rural youth and access to land, rural women and the gender issue, the Earth Forum in Caruaru (Brazil), Nitlapan success stories, and a forum on land grabbing for the production of pineapples and African palm on the Costa Rica-Nicaraguan border.

[25] Juan XXIII Institute of Social Action was founded in 1962 to help build homes and extend health services for the poor.

[30][31][32] The institute helped in the reconstruction of Cusmapa after the Hurricane Mitch[33] and in 2011 teamed with CAFOD to lend assistance to Villa El Carmen.

[38] Institute of History of Nicaragua and Central America (IHNCA), opened in September 1997, is housed in a three-storey building with research areas, auditoriums, exhibition halls, and documentary deposits.