Born in Osijek, in the Austro-Hungarian Kingdom of Croatia-Slavonia (present-day Croatia), he and his family moved to Zagreb in 1910; his father was a tailor and his mother a seamstress.

Šeper was also the President of the International Theological Commission from its inception in April 1969, and the author of the 1973 document Mysterium Ecclesiae,[1] which was written in order to re-orient the ecclesiology of the post-Vatican II period.

After the first meeting held on 11 April 1969 in the convent of the Divine Master in Ariccia, in the Vatican he supervised the development of work on the ecumenical dialogue between the Church and Freemasonry.

[2] In 1974, the Congregation published a "Declaration on procured abortion", re-asserting the Church's opposition to the procedure since the publication of Humanae Vitae.

[4] John Paul presided at his funeral Mass, and Šeper's body was later transferred to Zagreb, where it is buried beside the tomb of Cardinal Stepinac.