The Catholic Church in Azerbaijan is part of the worldwide Catholic Church, under the spiritual leadership of the Pope in Rome. There are about 570 local Roman Catholics in the country as of 2016. Azerbaijan is covered entirely by a single Apostolic Prefecture since 2011. The community is served by seven Salesian priests and two friars. In addition, there is a mission of the Missionaries of Charity.
Christians have been present in Azerbaijan since the 1st century AD. Starting from 1320, Catholic missionaries such as Jordanus and Odoric of Pordenone have visited what is now Azerbaijan and have established missions mostly in large cities. In the 14th century in Nakhchivan alone, there were 12 missions led by Dominicans, Capuchins, Augustinians, etc. In 1660 Superior of the Capuchin Mission at Isfahan, friar Raphaël du Mans reported Catholic parishes functioning in Baku and Shamakhi. Jesuits arrived and set a mission in Ganja in the 1680s.
In the 14th and 15th centuries, efforts of Bartholomew, a Dominican missionary from Bologna, resulted in the conversion of 28 settlements in Nakhchivan into Roman Catholicism. Despite hardships and pressure from the Armenian Apostolic Church, Catholicism survived here for over three centuries, after which it went into decline and by the 1800s was no longer practiced.
With the establishment of the Russian rule, these lands became a popular destination for members of various Christian denominations. Catholics were represented by ethnic Poles who started immigrating to Baku and Shemakhi in the mid-19th century, Ukrainians, Georgian Catholics, Armenian Catholics, as well as Western Europeans who stayed in Baku on a temporary or permanent basis.
The village of Siyaqut in Nakhchivan was founded in the 1850s by Assyrian immigrants from Salmas, Persia and remained the only Chaldean Christian village in the South Caucasus. Beginning in the 1880s, the priest serving in Siyaqut was ordained by the Roman Catholic bishop.
In the early 20th century there was a community in Baku made up of Polish, German, and Russian immigrants for whose needs the Church of the Immaculate Conception of the Blessed Virgin Mary was built in 1912. Another church was built in Qusar, where a Polish regiment had been quartered. In 1917, the community numbered 2,500 people. In the early 1930s, on the orders of the Stalinist government, the small community's only priest Stefan Demurov was executed. In 1931, the communist authorities demolished the church.
In 1997, a Slovak priest came to Baku to restart the community.
As Azerbaijan is a secular country the 1996 law stated that foreigners have freedom of conscience, but denied the right to "carry out religious propaganda", i.e., to preach, under the threat of fines or deportation. Rafig Aliyev, head of the State Committee for Work with Religious Organisations, had declared that this ban for the foreigners to conduct religious work will be amended. The law of the Republic of Azerbaijan (1992) "On freedom of faith" ensures the right of any human being to determine and express his view on religion and to execute this right.
On 11 October 2000, the mission sui iuris of Baku was established covering the whole of the country, with Daniel Pravda as its first superior. Pravda had worked in Siberia for many years when he became head of the mission, and noted that when he was first appointed, the church had no structure, and there were many problems with the government relating to visas, but when a new Religious affairs official was appointed, problems abated and preparations for a Papal visit gained traction. On May 23, 2002, Pope John Paul II visited the country, despite his increasingly fragile health. He was initially invited by Azerbaijan's president, Heydar Aliyev. Thanks to his visit, President Aliyev gave the Catholic Church a plot of land to build a church. The building was funded by proceeds from Pope John Paul II's book sales and foreign donations. Delegates from Azerbaijan attended the first Congress of Catholic Laity of Eastern Europe in 2003. When Archbishop Claudio Gugerotti, the apostolic nuncio to Azerbaijan, visited the country he encountered many elderly believers who had waited almost 70 years to receive the sacrament of confirmation. St Mary's Catholic Church of Baku, the only Catholic church in the country, was rebuilt, with work nearing its end in March 2007. It was inaugurated by Cardinal Secretary of State Tarcisio Bertone on 7 March 2008, 70 years after it had been shut down by the Soviets. The Mission of Baku became on 4 August 2011 the Apostolic Prefecture of Azerbaijan, with a Catholic population of 520. The Apostolic Prefect is the Salesian Father Vladimír Fekete, a Slovak like his predecessors Jozef Pravda and Jan Čapla. Only a few of the Catholics are Azeris, and the congregation's working languages are Russian and English. On April 29, 2011, an accord was reached between the Vatican and the government of Azerbaijan related to the relations of the two entities, and the various rights and freedoms of the Catholic Church and its personnel within the country.
In 2016, Behbud Mustafayev was ordained the first Roman Catholic deacon of Azeri origin by archbishop Paolo Pezzi.