Nevertheless, many Jews were given refuge during the war by the anti-Nazi resistance movement led by the marshal Josip Broz Tito, an ethnic Croat.

Today there are 9 synagogues with Jewish organizations in Croatia; Zagreb (x2), Rijeka, Osijek, Split, Dubrovnik, Čakovec, Daruvar and Slavonski Brod.

[6] Zagreb Faculty of Humanities and Social Sciences's Chair of Judaism offers undergraduate and graduate programs in Jewish studies.

Faced with harsh Soviet pressure, Czechoslovakia and Israel arranged a transfer through Yugoslavia's Nikšić Airport (in Montenegro) and Port of Rijeka (in Croatia) in the top secret Operation Velvetta.

Considering that Yugoslavia, which was stretched between the NATO and the Warsaw Pact during the Cold War, was a leader of the third bloc called Non-Aligned Movement and that President Tito maintained close relations with Arab leaders, especially Gamal Abdel Naser, since most Arab countries were members of the Movement, Yugoslavia severed all diplomatic relations with Israel in 1967 after Israel attacked Egypt in the Six-Day War.

[10][11] After the breakup of Yugoslavia occurred as a result of a series of political upheavals and conflicts during the early 1990s, conservative politician President Franjo Tuđman rose to power in the newly Republic of Croatia on 8 October 1991.

Israel has complained about the attitude that Tuđman presented in his book "The Wastelands of Historical Reality", more specifically in the chapter entitled "The history of the multiplication of war crimes and the creation of the Jasenovac and Bleiburg myth" in which he questioned the number of people killed in Jasenovac concentration camp considering that the number was from 30,000 to 40,000, unlike much higher figures presented by the Yugoslav authorities which emphasized a range between 350,000 and 800,000.

[12] The United States Holocaust Memorial Museum (USHMM) presently estimates that the Ustaša regime murdered between 77,000 and 99,000 people in Jasenovac between 1941 and 1945, out of which 12,000 to 20,000 were Jews.

In September 1997, after several months of intense negotiations, Israel and Croatia published a joint statement on intention to establish diplomatic relations.

Secret talks between the Israeli Foreign Ministry Director-General Eitan Bentsur, and the head of the office of the Croatian president Hrvoje Šarinić were held in Budapest.

Full diplomatic relations among two countries were established on September 4, 1997, after Croatian government issued a statement apologizing for the crimes committed by Ustaše in the NDH while President Tuđman promised to publish a modified version of his book.

[20] Croatian producer Branko Lustig said on March 4, 2015, in an interview for the Slovenian television that he first met President Tuđman on Zagreb premiere of the film Schindler's List in 1994.

"[21] Croatian historian Slavko Goldstein said in an interview for Jutarnji list that he asked for an audience with President Tuđman when he saw a film about Bruno Bušić that was pro-Ustasha intoned in the early 1990s.

[citation needed] In January 2001, the two countries mutually abolished visas while in October of the same year, president Mesić visited Israel and apologized for the Ustaše crimes against the Jewish people committed during the WWII.

On 15 February 2012, Croatian president Ivo Josipović visited Israel and apologized for the Ustaše crimes against the Jewish people committed during the WWII.

She stated in Yad Vashem: "As president of Croatia, I express my deepest regret to all the victims of the Holocaust that were killed by the hands of the collaborationist Ustasha regime during World War II.

Croatian director Branko Lustig visited Israel with the president Grabar-Kitarović and gave an Oscar he won for the film Schindler's List as a gift to the Yad Vashem.

[28][29] On 26 October 2016, UNESCO's World Heritage Committee passed a controversial resolution on Temple Mount which dismissed Israeli connections to the location.

Before the meeting opened, Palestinian Authority and Jordan wanted to present resolution text which would strengthen the Muslim claims to the Temple Mount, but after they were ensured that there was a consensus vote on the existing, softer version of the text, they submitted it, but when the meeting opened, Croatia and Tanzania called for a secret ballot which effectively blocked a unanimous by consensus vote.

Croatia joined Cyprus, Greece, Italy, Russia and Turkey in fighting November 2016 Israel wildfires by sending its 2 Canadair CL-415 water bombers.

During their meeting, two prime ministers praised the significant progress of bilateral relations between two nations in the past years and signed a joint statement on the intention between the Croatian and Israeli governments on co-operation in the field of disaster prevention and emergency response.

Prime minister Plenković said that they primarily talked about the improvement of economic and political relations between their countries, especially "agriculture and Mediterranean cooperation."