The center was established in June 1959, through the formula of aggregation to high school 'Utriusque Iuris' of the Pontifical Lateran University.

The official inauguration took place on October 7 and was the main part of the opening of the academic year of the Estudio General de Navarra. The event was very solemn and was presided over by the Nuncio of His Holiness in Spain, Bishop Hildebrando Antoniutti.

The day after the solemn inauguration, on October 8, 1959, the classes of high school began in a classroom of the Chamber of Comptos.

On October 25, 1960, in the conference room Capitular of the Cathedral of Pamplona, the solemn erection of the University took place, and the high school became School of Canon Law, the first School of Ecclesiastical Sciences of the new University.

Once the teaching was launched, the task of publishing a journal was immediately undertaken. The second academic year began with this exciting project, which became a reality in January 1961 with the publication of the first issue of 'Ius Canonicum'.

On June 25, 1962, Javier Hervada defended his thesis "Fin y características del ordenamiento canónico" directed by Pedro Lombardía. It was the first thesis at Canon Law; and also, the first one defended at the University.

On October 7, 1967, St. Josemaría, as Chancellor of the University of Navarra, presented the doctorate 'Honoris Causa' to the canonist Willy Onclin (Limburg, 1905-Louvain, 1989).

In his speech, Onclin publicly expressed the positive evaluation he had of the work of the people of the School of Canon Law. These were his words:
"The teachers of this School defend the real value that constitutes the Canon Law in the Church [...]. I am happy to be able from now on to unite my efforts to those of the masters of this School for the realization of our common ideal: to seek the truth, to serve the just, to bring people together and thus to build a better world".

On March 28, 1967, the high school Martín de Azpilcueta, a scientific research center under the auspices of the School of Canon Law was established.

In 1975 began the construction of the current building of the Schools Ecclesiastical, designed by the architect Joan Rius. The 76/77 academic year began in the new building, where the classes of the School of Canon Law were moved.

In 1976, School hosted the III International congress at Canon Law. It hosted the 10th edition of congress again in 1998.

The high school Martín de Azpilcueta, of the University of Navarra, with the partnership of the department of Education and Culture of the Government of Navarra, organized some conference of programs of study about Doctor Navarro on June 21, 1986, the IV centenary of his death.

The event was attended by scholars of Church Law and Moral Theology, together with historians of the Modern Age, of International Law and of the Economics.

In 1996 was published the Exegetical Commentary to the Code of Canon Law: 6 volumes, promoted by high school Martín de Azpilcueta, coordinated and directed by professors Angel Marzoa, Jorge Miras and Rafael Rodríguez-Ocaña.

On December 6, 1998, the Ministry of Justice awarded Professor Javier Hervada Xiberta (Barcelona, 1934-Pamplona, 2020) the San Raimundo de Peñafort Cross of Honor. The ceremony, presided over by the President Magnificent, took place in the Hall of Degrees of Office of the Executive Council on February 25, 1999.

Since 1965 he was Full Professor of Canon Law of the University of Navarra, of whose School of Law he was Dean between 1973 and 1984.

The magazine of the School 'Ius Canonicum' publishes its issue 100 on the 50th anniversary of the academic center. Edited biannually by high school Martín de Azpilcueta, Ius Canonicum was founded in 1961.

The volume opens with a commemoration of the issue 100, presented by its director, Jorge Otaduy, and includes two papers by Professors José Orlandis and Gaetano Lo Castro, entitled "The high school of Canon Law of the Estudio General de Navarra" and "St. Josemaría Escrivá, Law, Justice. (Fifty years after the creation of the School of Canon Law of the University of Navarra)".

Hungarian Cardinal Péter Erdö (Budapest, 1952), Archbishop of Budapest and President of the committee of Bishops' Conferences of Europe, was invested to receive honorary doctor by the School of Canon Law on October 27, 2011.

The godfather of the new doctor, Professor Eduardo Molano, noted that despite being one of the youngest cardinals of the current high school Cardinalate, "he already has a long history of service to the Church, in which his excellent theological and legal preparation has contributed to make him a great pastor and man of government".

In 2012, the School published the "Diccionario General de Canon Law". The work, which required ten years of dedication, is composed of 7 volumes and 2,118 voices. A total of 583 authors from 33 countries worked on it.

The high school Martín de Azpilcueta published in early February 2019 the complete works of Professor Javier Hervada. These are the first opera omnia of the digital collection 'Obras completas de autores' of the School.

In 2019 'Ius Canonicum' obtained the Quality Seal of the Spanish Foundation for Science and Technology (FECYT).

A year later, in 2020, the journal was listed for the first time in the Q1 quartile, in the category of 'programs of study religious' and 'Law', of Scimago Journal Rank.

In January 2023, deadline was opened to take the new Master's Degree in Canon Marriage Law, which will start in September, and combines work online and teaching face-to-face at campus in Madrid.

Álvaro González Alonso is the academic director of the program.