In January 1990, the League of Communists broke up on ethnic lines, with the Croatian and Slovene factions demanding a looser federation at the 14th Extraordinary Congress.

In February 1990, Jovan Rašković founded the Serb Democratic Party (SDS) in Knin, whose program aimed to change the regional division of Croatia to be aligned with ethnic Serb interests.

On 4 March 1990, 50,000 Serbs rallied at Petrova Gora and shouted negative remarks aimed at Tuđman, chanted "This is Serbia", and expressed support for Milošević.

The first free elections in Croatia and Slovenia were scheduled for a few months later. The first round of elections in Croatia was held on 22 April, and the second round on 6 May.

A tense atmosphere prevailed on May 13, 1990, when a football game was held at Zagreb in Maksimir Stadium between Zagreb's Dinamo team and Belgrade's Red Star. The game erupted into violence between the Croatian and Serbian fans and with the police.

On 14 May 1990, the weapons of the TO of Croatia, in Croat-majority regions, were taken away by the JNA, preventing the possibility of Croatia having its own weapons as was done in Slovenia. Borisav Jović, Serbia's representative in the Federal Presidency and a close ally of Slobodan Milošević, claimed that this action came at the behest of Serbia.

On 30 May 1990, the new Croatian Parliament held its first session.

According to Jović, on 27 June 1990 he and Veljko Kadijević, the Yugoslav Defense Minister, met and agreed that they should, regarding Croatia and Slovenia, "expel them forcibly from Yugoslavia, by simply drawing borders and declaring that they have brought this upon themselves through their decisions". According to Jović, the next day he obtained the agreement of Milošević.

After the election of Tuđman (Croatian President) and the HDZ, a Serb Assembly was established in Srb, north of Knin, on 25 July 1990 as the political representation of the Serb people in Croatia. The Serb Assembly declared "sovereignty and autonomy of the Serb people in Croatia".

In August 1990, an unrecognized mono-ethnic referendum was held in regions with a substantial Serb population which would later become known as the Republic of Serbian Krajina (RSK) (bordering western Bosnia and Herzegovina) on the question of Serb "sovereignty and autonomy" in Croatia.

On 21 December 1990, the SAO Krajina (Serbian Autonomous Oblast of Krajina) was proclaimed by the municipalities of the regions of Northern Dalmatia and Lika, in south-western Croatia. Article 1 of the Statute of the SAO Krajina defined the SAO Krajina as "a form of territorial autonomy within the Republic of Croatia" in which the Constitution of the Republic of Croatia, state laws, and the Statute of the SAO Krajina were applied.

On 22 December 1990, the Parliament of Croatia ratified the new constitution, which was seen by Serbs as taking away rights that had been granted by the Socialist constitution.

The conflict escalated into armed incidents in the majority-Serb populated areas. The Serbs attacked Croatian police units in Pakrac in early March.

Josip Jović is widely reported as the first police officer killed by Serb forces as part of the war, during the Plitvice Lakes incident in late March 1991.

On 12 March 1991, the leadership of the Army met with the Presidency of the SFRY in an attempt to convince them to declare a state of emergency which would allow for the army to take control of the country.

The Croatian military was in a much worse state than that of the Serbs. In the early stages of the war, lack of military units meant that the Croatian Police force would take the brunt of the fighting. The Croatian National Guard, the new Croatian military, was formed on 11 April 1991, and gradually developed into the Croatian Army by 1993.

In Tovarnik, a Croat policeman was killed by Serb paramilitaries on 2 May.

While in Sotin, a Serb civilian was killed on 5 May when he was caught in a crossfire between Serb and Croat paramilitaries.

On 6 May, the 1991 protest in Split against the siege of Kijevo at the Navy Command in Split resulted in the death of a Yugoslav People's Army soldier.

On 15 May, Stjepan Mesić, a Croat, was scheduled to be the chairman of the rotating presidency of Yugoslavia. Serbia, aided by Kosovo, Montenegro, and Vojvodina, whose presidency votes were at that time under Serbian control, blocked the appointment, which was otherwise seen as largely ceremonial.

On 19 May 1991, the Croatian authorities held a referendum on independence with the option of remaining in Yugoslavia as a looser union. Serb local authorities issued calls for a boycott, which were largely followed by Croatian Serbs. The referendum passed with 94% in favor.

The newly constituted Croatian military units held a military parade and review at Stadion Kranjčevićeva in Zagreb on 28 May 1991.

The parliament of Croatia declared Croatia's independence and dissolved its association with Yugoslavia on 25 June 1991.

In June and July 1991, the short armed conflict in Slovenia.

In August 1991, the Croatian Army had fewer than 20 brigades.

In August 1991, the Battle of Vukovar began. The Battle of Vukovar was an 87-day siege of Vukovar in eastern Croatia by the Yugoslav People's Army (JNA), supported by various paramilitary forces from Serbia, between August and November 1991. Before the Croatian War of Independence the Baroque town was a prosperous, mixed community of Croats, Serbs and other ethnic groups. As Yugoslavia began to break up, Serbia's President Slobodan Milošević and Croatia's President Franjo Tuđman began pursuing nationalist politics. In 1990, an armed insurrection was started by Croatian Serb militias, supported by the Serbian government and paramilitary groups, who seized control of Serb-populated areas of Croatia. The JNA began to intervene in favour of the rebellion, and conflict broke out in the eastern Croatian region of Slavonia in May 1991. In August, the JNA launched a full-scale attack against Croatian-held territory in eastern Slavonia, including Vukovar.

The Arbitration Commission of the Peace Conference on Yugoslavia, also referred to as Badinter Arbitration Committee, was set up by the Council of Ministers of the European Economic Community (EEC) on August 27, 1991, to provide the Conference on Yugoslavia with legal advice.

This move followed months of standoff for JNA positions in Dalmatia and elsewhere now known as the Battle of the barracks.

It also coincided with the end of Operation Coast-91, in which the JNA failed to occupy the coastline in an attempt to cut off Dalmatia's access to the rest of Croatia.

On October 3, the Yugoslav Navy renewed its blockade of the main ports of Croatia.

On October 5, President Tuđman made a speech in which he called upon the whole population to mobilize and defend against "Greater Serbian imperialism" pursued by the Serb-led JNA, Serbian paramilitary formations, and rebel Serb forces.

On 7 October, the Yugoslav air force attacked the main government building in Zagreb, an incident referred to as the bombing of Banski dvori.

The next day, as a previously agreed three-month moratorium on implementation of the declaration of independence expired, the Croatian Parliament severed all remaining ties with Yugoslavia. 8 October is now celebrated as Independence Day in Croatia.

On 15 October after the capture of Cavtat by the JNA, local Serbs led by Aco Apolonio proclaimed the Dubrovnik Republic.

Croatian forces made further advances in the second half of December, including Operation Orkan 91 which was a military offensive undertaken by the Croatian Army (Hrvatska vojska – HV) against the Yugoslav People's Army (Jugoslovenska Narodna Armija – JNA) and SAO Western Slavonia Territorial Defense Forces in the Sava River valley, in the region of Western Slavonia during the Croatian War of Independence. The operation began on 29 October 1991 and ended on 3 January 1992 when a nationwide ceasefire was signed to implement the Vance plan. The offensive was aimed at recapturing the region, in conjunction with two other HV offensives launched against SAO Western Slavonia in the north of the region within days.

Operation Otkos 10 (31 October to 4 November) resulted in Croatia recapturing an area between the Bilogora and Papuk mountains.

The Croatian army began a successful counterattack in early November 1991, its first major offensive operation of the war.

On 14 November, the Navy blockade of Dalmatian ports was challenged by civilian ships. The confrontation culminated in the Battle of the Dalmatian channels, when Croatian coastal and island based artillery damaged, sank, or captured a number of Yugoslav navy vessels, including Mukos PČ 176, later rechristened PB 62 Šolta.

On December 19, as the intensity of the fighting increased, Croatia won its first diplomatic recognition by a western nation—Iceland—while the Serbian Autonomous Oblasts in Krajina and western Slavonia officially declared themselves the Republic of Serbian Krajina.

On December 21, 1991 for the first time in the war Istria was under attack.

On December 26, 1991, the Serb-dominated federal presidency announced plans for a smaller Yugoslavia that could include the territory captured from Croatia during the war.

Croatia lost much territory, but expanded the Croatian Army from the seven brigades it had at the time of the first ceasefire to 60 brigades and 37 independent battalions by December 31, 1991.

A new UN-sponsored ceasefire, the fifteenth in just six months, was agreed on January 2, 1992, and came into force the next day.

This so-called Sarajevo Agreement became a lasting ceasefire. Croatia was officially recognized by the European Community on January 15, 1992.

The UNPROFOR (United Nations Protection Force) was officially created by UN Security Council Resolution 743 on February 21, 1992.

Operation Jaguar at Križ Hill near Bibinje and Zadar, on May 22, 1992.

Croatia became a member of the UN on May 22, 1992, which was conditional upon Croatia amending its constitution to protect the human rights of minority groups and dissidents.

A series of military actions in the Dubrovnik hinterland: Operation Tigar, on 1–13 July 1992.

In 1992, the Croat-Bosniak conflict erupted in Bosnia and Herzegovina, just as each was fighting with the Bosnian Serbs. The war was originally fought between the Croatian Defense Council and Croatian volunteer troops on one side and the Army of the Republic of Bosnia and Herzegovina (ARBiH) on the other, but by 1994, the Croatian Army had an estimated 3,000 to 5,000 troops involved in the fighting.

The Croatian army launched Operation Maslenica, an offensive operation in the Zadar area on January 22.

On February 18, 1993, Croatian authorities signed the Daruvar Agreement with local Serb leaders in Western Slavonia. The aim of the secret agreement was normalizing life for local populations near the frontline. However, authorities in Knin learned of this and arrested the Serb leaders responsible.

The International Criminal Tribunal for the former Yugoslavia (ICTY) was established by UN Security Council Resolution 827, which was passed on 25 May 1993.

In June 1993, Serbs began voting in a referendum on merging Krajina territory with Republika Srpska.

Operation Medak Pocket took place in a salient south of Gospić, from September 9–17. The offensive was undertaken by the Croatian army to stop Serbian artillery in the area from shelling nearby Gospić.

Under pressure from the United States, the belligerents agreed on a truce in late February, followed by a meeting of Croatian, Bosnian, and Bosnian Croat representatives with US Secretary of State Warren Christopher in Washington, D.C. on February 26, 1994.

On March 4, Franjo Tuđman endorsed the agreement providing for the creation of Federation of Bosnia and Herzegovina and an alliance between Bosnian and Croatian armies against the Serb forces.

On November 21, NATO attacked the Udbina airfield controlled by the RSK, temporarily disabling runways. Following the Udbina strike, NATO continued to launch strikes in the area.

On November 23, after a NATO reconnaissance plane was illuminated by the radar of a surface-to-air missile (SAM) system, NATO planes attacked a SAM site near Dvor with AGM-88 HARM anti-radiation missiles.

From November 29 – December 24 in the Winter '94 operation near Dinara and Livno. These operations were undertaken to detract from the siege of the Bihać region and to approach the RSK capital of Knin from the north, isolating it on three sides.

From 25–30 July, the Croatian Army and Croatian Defense Council (HVO) troops attacked Serb-held territory north of Mount Dinara, capturing Bosansko Grahovo and Glamoč during Operation Summer '95.

On 4 August, Croatia started Operation Storm, with the aim of recapturing almost all of the occupied territory in Croatia, except for a comparatively small strip of land, located along the Danube, at a considerable distance from the bulk of the contested land. The offensive, involving 100,000 Croatian soldiers, was the largest single land battle fought in Europe since World War II. Operation Storm achieved its goals and was declared completed on 8 August.

Further combat was averted on 12 November when the Erdut Agreement was signed by the RSK acting defense minister Milan Milanović, on instructions received from Slobodan Milošević and Federal Republic of Yugoslavia officials.

The new UN mission was established as the United Nations Transitional Authority for Eastern Slavonia, Baranja and Western Sirmium (UNTAES) by United Nations Security Council Resolution 1037 of 15 January 1996.

As the UNTAES replaced the UNCRO mission, Prevlaka peninsula, previously under UNCRO control, was put under control of United Nations Mission of Observers in Prevlaka (UNMOP). The UNMOP was established by United Nations Security Council Resolution 1038 of 15 January 1996, and terminated on 15 December 2002.

The transitional period was subsequently extended by a year. On 15 January 1998, the UNTAES mandate ended and Croatia regained full control of the area.