Çeku is an ethnic Albanian who served as an officer in the Croatian Army during the Croatian War of Independence against the breakaway Republic of Serbian Krajina, and was military commander of the KLA during the 1998-1999 Kosovo War, and then commanded the Kosovo Protection Corps under the United Nations Interim Administration Mission in Kosovo.
After Agim Çeku finished the secondary military school in Belgrade, he attended the Zadar Military Academy. Shortly afterwards, he joined the Yugoslav People's Army (JNA) as an artillery captain. In 1991 the Yugoslav wars broke out and he deserted from the JNA and joined the Croatian National Guard, when the Republic of Croatia found itself at war in breaking away from Yugoslavia.
He was closely involved in the subsequent Croatian War against the breakaway Republic of Serbian Krajina. He participated in several military operations, he first was in Operation Maslenica when he was the head of Velebit's artillery section, from January to February 1993, Operation Medak pocket near Gospic, in which he was wounded, and Operation Storm in August 1995 that captured most of the Krajina territory. Subsequently he continued the advance as head of Croatian forces into the Republic of Bosnia and Herzegovina fighting in western Bosnia against the forces of the Serb Republic in Operation Maestral.
After the war the Croatian Army was reformed and President Franjo Tuđman named Çeku commanding officer of the Fifth District Region in Rijeka. In 1998 he filed request for retirement to go to Kosovo to join the Kosovo Liberation Army with which it maintained links, which was fulfilled in 1999.
Çeku developed contacts with the KLA, a guerrilla group fighting Serbian rule in Kosovo, some time in the mid-1990s. He resigned from the Croatian Army in February 1999. When the Kosovo War broke out in March 1999, the KLA initially did very badly against Serbian/Yugoslav forces, due in part to poor leadership under its senior commander Suleiman Selimi, a militarily inexperienced individual who had been given the post largely because of his influence in the Drenica region (the KLA's heartland).
In May 1999, Çeku was appointed the KLA's chief of staff, replacing Selimi. He immediately set about reorganising the KLA and implementing a proper military structure within the organization. In the closing days of the Kosovo War, the KLA began providing systematic intelligence to NATO as well as mounting attacks to lure Serbian forces into the open, enabling NATO warplanes to bomb them. According to reports at the time, Çeku was the principal liaison between NATO and the KLA.
Following the end of the war in June 1999, Çeku oversaw the demilitarisation of the KLA and its transformation into the Kosovo Protection Corps (KPC), an ostensibly civilian organization charged with disaster response, demining, search and response and humanitarian projects. Although the international community insisted the KPC was a civilian organization, Çeku and its membership said they believed the KPC should evolve into the future army of an independent Kosovo. Çeku managed ably many difficult challenges for the KPC, including allegations that its members were supporting the ethnic Albanian insurgency in Macedonia in 2001
The Serbian Government claims that Çeku is a war criminal, though Serbia's jurisdiction in the matter is not recognised by the United Nations. Though Çeku has not been the subject of any ICTY indictment, he was briefly detained in Slovenia in October 2003 and in Hungary in March 2004 on the basis of an Interpol warrant issued by Serbia. Çeku was quickly released in both instances following pressure by the United Nations Interim Administration Mission in Kosovo (UNMIK). The International Criminal Tribunal for the former Yugoslavia (ICTY) issued the last indictments in late 2004 and limited all further investigations to ongoing cases only.
Colombian authorities have expelled Ceku from a conference held in the country because Serbia requested his extradition because of possible war crimes committed by him during the Kosovo War.
On 23 June 2009 he was arrested in Bulgaria under the Interpol arrest warrant issued by Serbia for alleged war crimes in Kosovo against non-Albanian population. The Bulgarian authorities decided to release him from custody, but requested that he remain in the country for up to 40 days as officials consider the extradition request from Serbia to face charges of genocide. On 30 June, he returned to Kosovo, after the Bulgarian prosecutors decided not to appeal the court's decision for his release.
On 10 March 2006, Çeku was elected Prime Minister of Kosovo by the Kosovo Assembly. After being sworn in, he declared his support for Kosovo independence, whilst promising to protect the rights of the Serbian minority. Çeku's appointment was backed by former Prime Minister Ramush Haradinaj, who resigned in early 2005 after the ICTY had indicted him for war crimes. In his first one hundred days in office, Çeku prioritized the implementation of the UN-endorsed "Standards" for good governance and multi-ethnicity, earning praise from UN Kosovo chief Søren Jessen-Petersen and Contact Group countries. On 24 July 2006, Çeku traveled to Vienna for the first high-level meeting between the Presidents and Prime Ministers of Serbia and Kosovo to discuss Kosovo's future status.
He stated that he would found a new political party after stepping down as PM, dispelling rumours that he would join the Reformist Party ORA. However, he joined the Social Democratic Party of Kosovo on 10 April 2008, and did not rule out that the party would unify with ORA.
On 23 February 2011, Çeku was made Minister of Security Forces of Kosovo.
He is married to Dragica, who is half-Serbian, half-Croatian. They have three children and the family divides its time between Pristina and the Croatian town of Zadar.