He was very active in the cause of Christian unity as president of the Willibrord Association (which promoted ecumenism in Holland) and in 1951 organized a Catholic conference on ecumenical questions.

On June 24, 1960 Pope John XXIII named him Secretary of the newly established Secretariat for the Union of Christians. During the work of the Second Vatican Council, he assisted Cardinal Augustin Bea in the preparation of the documents on ecumenism (Unitatis Redintegratio), religious liberty (Dignitatis Humanae), and relations with non-Christian religions (Nostra Aetate).

On April 12, 1969 Pope Paul VI appointed him President of the Secretariat for the Union of Christians, in which he capacity he served for twenty years. His duties included presiding over the Commission for Religious Relations with the Jews, and thus he oversaw the composition of two important documents: "Guidelines and Suggestions for Implementing the Conciliar Declaration, Nostra Aetate, No. 4" (1974) and "Notes on the Correct Way to Present Jews and Judaism in Preaching and Teaching in the Roman Catholic Church" (1985). He was also instrumental in arranging the historic visit of Pope John Paul II to the Great Synagogue of Rome on April 13,1986.

Known at the Vatican as "The Flying Dutchman" for his extensive travels in the service of ecumenism, he published in 1992, Church and Jewish People: New Considerations, a collection of his essays from 1975-1990. In 2003 the International Council of Christians and Jews awarded him its Sir Sigmund Sternberg Award for his groundbreaking contributions to Christian-Jewish relations.

In failing health, Willebrands went in 1997 to a Franciscan convent in the Netherlands, where he remained until his death.

The Center joins in mourning the death, but also in being grateful for the great service, of this pioneer in interfaith amity.