Diplomatic relations among the two countries were established on February 8, 1992, following Croatia's independence from SFR Yugoslavia, although they date far back in history.

According to the work De Administrando Imperio written by the 10th-century Byzantine Emperor Constantine VII, the Croats had arrived in what is today Croatia in the early 7th century AD.

Some, like Franjo Rački, Nada Klaić, and Tadija Smičiklas, consider it to be fake, while others, like Ferdo Šišić, believed that it is legitimate mostly due to the style of writing which matches with that of the Roman Curia.

Pope John VIII replied with a letter on June 7, 879, in which he wrote that he celebrated a Mass at the tomb of St. Peter at which he invoked God's blessing on Branimir and his (Croatian) people.

[5] During the Croatian–Ottoman Wars that lasted from the 15th to 19th century Croats strongly fought against the Turks which resulted in the fact that the westernmost border of the Ottoman Empire and Europe became entrenched on the soil of the Croatian Kingdom.

Negotiations on the concordat between the Kingdom and the Holy See were led in 1936 by the Yugoslav Minister of Justice Ljudevit Auer and Cardinal Eugenio Pacelli (who later become Pope Pius XII).

[9] British writer Peter Hebblethwaite wrote that Pavelić was anxious to get diplomatic relations and a Vatican blessing for the new Catholic state but that "neither was forthcoming" because the Holy See has been linked to its traditional practice of not recognizing newly created entities during wartime.

However, Edmond Paris notes that Aloysius Stepinac wanted Croatia's independence from the Serb dominated Yugoslavia which he considered to be "the jail of the Croatian nation" so he arranged an audience between Pavelić and Pope Pius XII.

Pope Pius XII, wishing to pay tribute to archbishop Stepinac for his faithfulness, elevated him to the College of Cardinals in 1953, which triggered a reaction from the Yugoslav government.

According to the Croatian diplomat and Vatican analyst Vjekoslav Cvrlje who served as a first Ambassador of Yugoslavia to the Holy See, President Tito was given special attention by the Pope.

During his address to the Pope, Tito said: "Your Holiness, I'm especially pleased to have this opportunity to meet with you and to convey to you the assurance of a high respect from the people and government of Yugoslavia.

"[14][15] The highest ranking Croatian prelate in the Holy See was cardinal Franjo Šeper who served as a Prefect of the Congregation for the Doctrine of the Faith from 1968 to 1981.

After Croatia declared independence from SFR Yugoslavia in June 1991 due to a series of political upheavals and conflicts within the Federation, the Holy See, namely Pope John Paul II, become one of the most keen advocates of Croatian recognition by the international community.

Although the Holy See is cautious in recognizing new states, it announced on October 3, 1991, that its diplomacy was working actively on Croatian international recognition.

John Paul visited Croatia two more times; from October 2 to 4, 1998, during which he canonized Cardinal Stepinac at the Eucharistic celebration in the Croatian National shrine of Marija Bistrica, in front of about 500 thousand people, and he later celebrated Mass on the occasion of the 1700th anniversary of the city of Split; from June 5 to 9, 2003, during which he visited Krk, Rijeka, Zadar, Dubrovnik, Osijek, and Đakovo.