Çeku was born in Qyshk, a village near Peja, at the time part of the Socialist Autonomous Province of Kosovo of SR Serbia, SFR Yugoslavia.

After the war the Croatian Army was reformed and President Franjo Tuđman named Çeku commanding officer of the Fifth District Region in Rijeka.

When war broke out in Kosovo, the KLA initially did very badly against the Yugoslav forces, due in part to poor leadership under senior commander Sylejman Selimi, a militarily inexperienced individual who had been given the post largely because of his influence in the Drenica region (the KLA's heartland).

[citation needed] Çeku managed ably many difficult challenges for the KPC, including allegations that its members were supporting the ethnic Albanian insurgency in Macedonia in 2001.

After being sworn in, he declared his support for Kosovo independence, whilst promising to protect the rights of the Serbian minority.

[7] 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.

[11] Although 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.