The Catholic Church in Estonia was organized as an Apostolic Administration in 1924 by Pope Pius XI. Today, it is the oldest Apostolic Administration in the world. The first Bishop of Estonia after the Protestant Reformation was a German Jesuit, Archbishop Eduard Profittlich S.J., who was consecrated in 1936 and later deported to Siberia in 1941: he died as prisoner in February 1942. His beatification process is still in progress. For 63 years, there have been no resident Catholic Bishops in Estonia. Currently, there is only an ecclesiastical district that is not part of any Bishops’ Conference.

In 1999, the Concordat between the Holy See and the Estonian Republic was signed: a remarkable occurrence in a country with a Lutheran tradition.

On September 10 in 2013, the local Church celebrated the 20th anniversary of saint John Paul II’s visit to Estonia (09.10.1993): an event that had a remarkable resonance in the country at that time.

On September 2015, 800 years have passed since Estonia and North Latvia were consecrated to the Virgin Mary - one of the oldest consecrations of a territory to the Mother of God. In 1215 Pope Innocent III stated at the Fourth Lateran Council that Estonia and Livonia had been consecrated to the Mother of God and that he wanted to promote the Mother's Land as well as the Son's Land - sicut terram filii, sic et terram matris. On September 6th 2015, the Estonian Apostolic Administrator Bishop Philippe Jourdan, together with Archbishop Zbignievs Stankevics of Riga, renewed this dedication to the Mother of God in accordance with the tradition of the Roman Catholic Church.