Formal diplomatic relations between the Holy See and the State of Israel were established on 30 December 1993 after the adoption of a "Fundamental Agreement" between the two states. A Vatican nunciature in Israel and an Israeli embassy in Rome were simultaneously opened on 19 January 1994. From the Vatican's point of view, the establishment of diplomatic relations between the two states is part of the Christian–Jewish reconciliation and, from the Israeli point of view, the normalization of diplomatic relations. Before diplomatic relations were established, the interests of the Catholic Church in Israel were looked after by the Apostolic Delegate to Jerusalem and Palestine, the Latin Patriarch of Jerusalem and the Custodian of the Holy Land, all of which continue to function.

Andrea Cordero Lanza di MontezemoloAndrea Cordero Lanza di Montezemolo previously served as the Apostolic Delegate to Jerusalem and Palestine. was appointed as the first Apostolic Nuncio to Israel, Shmuel Hadas was appointed first Israeli Ambassador to the Holy See, in September of that year.

Since 3 June 2021, the Nuncio to Israel has been Adolfo Tito Yllana. The present Israeli ambassador to the Vatican is Raphael Schutz. Oren David was the Ambassador from 2016 to 2021, and Zion Evrony was the Ambassador from 30 September 2012 to 2016. He followed Mordechay Lewy, who was appointed in May 2008, Oded Ben-Hur (from June 2003), Yosef Neville Lamdan (from September 2000), Aharon Lopez (from April 1997), and Shmuel Hadas (from September 1994).

Fundamental Agreement

On 30 December 1993, the Holy See and Israel signed two agreements—the Fundamental Agreement Between the Holy See and the State of Israel and an Additional Protocol. The Fundamental Agreement is seen as a concordat that deals with tax exemptions and property rights of the Catholic Church and related entities within Israeli territory that entered into force on 10 March 1994, but has not been ratified by the Knesset. The Additional Protocol details provisions related to the establishment of normal diplomatic ties between the Holy See and Israel, pursuant to which the Holy See established on 15 June 1994 full diplomatic relations with Israel. Press briefing: Establishment of diplomatic relations with the Holy See The Holy See set up an Apostolic Nunciature to Israel in Tel Aviv, and appointed an Apostolic Nuncio. Several outstanding issues had still to be resolved, and have still to be resolved.

On 10 November 1997, the Holy See and Israel entered into a further agreement, titled Legal Personality Agreement Between the State of Israel and the Holy See,Agreement Between the State of Israel and the Holy See but this agreement has also not been ratified by the Knesset. Under the 1997 agreement, Israel would recognise the juridical personality and the authority of canon law within the Catholic Church and its institutions, as well as those of the Latin Patriarchate of Jerusalem and of the Eastern Catholic Patriarchates and their respective dioceses in Israeli territory, and the recognition of prevailing Israeli law in civil and criminal matters."Israel-Vatican Diplomatic Relations" on the Israeli Foreign Ministry web site

Diplomatic relations are tense due to the non-resolution of the accords relating to property rights and tax exemptions for the Church in Israel, the political activism of clergy in Israel and the Palestinian Authority, and the interplay between Israel-Vatican relations – on one hand – and the Jewish-Catholic inter-religious dialogue – on the other. The main concerns of the Vatican in Israel is the protection of the Latin Church Catholic churches, its properties and assets, and of the Holy places. Israel, for its part, has taken offence at several matters regarded by the Vatican as internal issues but which are seen by Israel and Jews around the world as of religious and historical consequence. These issues include the beatification of Pope Pius XII despite his failure to speak out against the Holocaust while it was still happening, the pardoning of a Holocaust-denying priest, and the subordination of inter-religious dialogue to evangelical aims.the subordination of inter-religious dialogue to evangelical aims

The unique character of Holy See—Israel relations While the Vatican has had diplomatic relations with Israel since 1993, it does not endorse a theological basis for the support of the state. Diplomatically, the Vatican views Israel's ambassador as a representative of Israel and not of the Jewish people and, if he accompanies a religious delegation, the Jewish religious leaders present must be Israeli citizens. Any similar delegation composed of non-Israeli Jews would be accompanied by the respective national ambassador.

For Israel, as with most states, the ability to assess diplomatic relations with a state that is lacking economic relations, cannot be quantifiable. Furthermore, since the Vatican is not a full member of any international organisation but only an observer and since official Vatican statements are phrased in extremely nuanced language, much public diplomacy requires interpretation of papal statements. Thus, to understand this unique relationship, traditional parameters must be replaced with a framework that employs a totally different set of parameters:Pope Benedict XVI within the context of Israel and Holy See relations; Mordechay Lewy, Israel Affairs XVI, Routledge 2010

First parameter – scope of representation The Nuncio has a rank of archbishop, and has both diplomatic and ecclesial functions. Besides his religious functions, the Nuncio also cares about the well-being of all Catholics in Israel, and intervenes on their behalf with the authorities. In this respect, the Nuncio's relations with government authorities overlap with the prerogatives of the Latin Patriarchate of Jerusalem.

Second parameter – diplomatic v. ecclesial duties The Nuncio's has both diplomatic and ecclesial duties. When he requests to enter an area of restricted accessibility for the purpose of holding mass, he is making a request in the name of religious freedom. Once his request is respected, it is regarded as a political gesture, meeting the expectations of religious freedom, but also in order to maintain friendly bilateral relations. If, however, he speaks to the media about his visit upon his return, it may be seen as a political and not as a spiritual act. This interplay enables using political tools to ease theological tensions that cannot be solved without one side or the other disavowing his faith.

Third parameter – freedom of religion v. security The opposite case would involve, for example, the issuance of visas one acceptable gauge of measuring relations between states, which should ideally be a transparent process. Extending visa permits to Catholic clergy is, for the Vatican, a matter of exercising freedom of religion. If, however, a clergy holds passports from states that are at war with, or do not recognize Israel, the matter is regarded by Israeli authorities rather as a security issue. The result of one side's existential caution may be seen by the other side as an infringement upon freedom of religion.

Bilateral relations

Visa policy In 2002, after the September 11 attacks and start of the Second Intifada, Israel adopted a more restrictive policy on permits for stays longer than three months. The change also applied to Christian clergy, who previously received permits in uncontrolled numbers and for practically indefinite periods. All previous permits were revoked and the number of permits was limited as were their duration. Each application was to be examined on its own merits.

In July 2012, Israel lifted all visa restrictions on Vatican passport holders. As of January 2025, all passport holders that do not require a Visa to travel to Israel need to apply for an Electronic Travel Authorization (ETA-IL). The change doesn't apply to clergy visas, but it would apply to non-diplomatic visa free travel for stays less than three months. On 31 December 2025, the Holy See umbrella charity organization Caritas Internationalis was one of 37 NGOs that did not meet the deadline to comply with enhanced security regulations and at least temporarily lost its license to operate in Israel. It responded by saying it would continue to operate and its status has been recognized by the Holy-See Israel agreement. However, it lost the ability to sponsor humanitarian visas.

Fiscal negotiations The longstanding negotiations of fiscal and property issues related to Catholic institutions in Israel have also proven to be complex: after a long break, negotiations were resumed in 2004, and since then, considerable progress has been achieved. Upon a Vatican suggestion, the dissemination of public statements is restricted to joint communiqués according to the principle that "nothing is agreed unless everything is agreed".

The subject to be negotiated is which tax and what is the degree of exemption that Catholic Church institutions should enjoy. Another issue to be dealt is which ecclesiastical property should enjoy what degree of immunity of expropriation. A sovereign state like Israel may well decide about present exemptions and immunities.

The Catholic Church however has an interest in safeguarding its presence and property until eternity by alleviating itself from any future financial burdens. These are highly complex issues in which, not only the Holy See is represented at the table, but also different local Catholic churches and institutions. Along the Israeli side of the table, four ministries are represented in the negotiations: Justice, Finance, Interior and Foreign Affairs. The latter leads the negotiations on behalf of the Israeli government. Some Israelis criticise the negotiations. It seems to them that Israel conducts an unfortunate 'give and give' equation and not a 'give and take' formula. Others see the benefit of speedy conclusion of the negotiations, as the relations might develop additional political dimensions.

The religious dimension Following the visit of Pope John Paul II, the framework of an inter-religious dialogue between the Chief Rabbinate of Israel and the respective Pontifical Council was established. The dialogue has taken place on an annual basis since 2003, meeting alternatively in Jerusalem and in the Vatican. It does not touch doctrinal matters of faith, but discusses various issues, such as bioethics, environmental problems, brain and clinical death, as well as matters pertaining to religious tolerance and violence. The annual meetings upgraded Israel's relations with the Holy See, as it gave the necessary theological symmetry to the formal diplomatic relations. The dialogue between the Vatican and the Rabbinate has proven to be a safety net in removing misunderstandings that cause theological tensions.

Israel's bilateral requests are limited by nature and do not touch upon any internal political issue of the Vatican. Even in the case of Pius XII's possible beatification, Israeli policy is to refrain from interfering in internal ecclesiastical affairs. It does, however, reserve its right to express its opinion on Pacelli's historical performance. With regard to this latter, Cardinal Walter Kasper mentioned the issue in his remarkable speech "Recent Developments in Jewish-Christian Relations", which he held at Hope University in Liverpool on 24 May 2010: