Prime Minister (2003–2006)
After the resignation of Palestinian prime minister Mahmoud Abbas on 6 September 2003, Palestinian Authority President Yasser Arafat nominated Qurei for the post of prime minister. Qurei accepted the nomination for the post in an "emergency government" on 10 September. The next day, the Israeli government, apparently in response to bombings two days earlier, released a statement, announcing the decision that President Arafat would be "removed." Qurei decided upon that to form a full government rather than a trimmed one.
On 5 October 2003, Qurei was appointed prime minister by presidential decree, and an eight-member emergency government was sworn in on 7 October. However, Qurei could not form a new cabinet because of a dispute with Arafat which lasted for 10 weeks over the choice of an interior minister and control of the Palestinian Security Services, and he threatened to resign. While the Fatah Central Committee had agreed to the emergency cabinet with Qurei as caretaker prime minister, the Fatah-dominated PLC refused to hold a vote of confidence. The emergency cabinet's term expired on 4 November but Arafat asked Qurei to remain in office despite their dispute, and the PLC approved a new 24-member government on 12 November. Among Qurei's top priorities was negotiating and meeting the road map for peace plan with Israel. Israel's non-compliance and the United States not having done enough to enforce Israeli compliance with the peace plan, along with a lack of internal support, had been reasons for Abbas' earlier resignation.
On 17 July 2004, he submitted his resignation amid growing chaos in the Gaza Strip. Offices of the Palestinian Authority in Gaza were burned down, and gunmen briefly abducted 4 French aid workers, the police chief and another official, demanding reforms. Arafat refused to accept Qurei's resignation. Arafat and Qurei disputed on Qurei's demand for more authority to restructure the security forces to reduce the growing turmoil. President Arafat decreed a State of Emergency in Gaza. On 27 July Arafat and Qurei held a press conference after reaching a settlement in a cabinet meeting. Qurei had retracted his resignation.
After Arafat's death in November 2004 and Mahmoud Abbas' subsequent victory in the 2005 Palestinian presidential election, Qurei was asked to continue in his post and form a new cabinet. Due to repeated demands by the Fatah officials and PLC members to make the new cabinet more reform-minded, the vote of confidence was repeatedly delayed. It was finally passed on 24 February 2005 after Qurei had revised the list of ministers to accommodate these demands.
On 15 December 2005, Qurei briefly resigned his prime ministership post to run for a seat in the Palestinian Legislative Council, but returned to office nine days later after deciding not to run. On 26 January 2006, Qurei announced his intention to resign following the Fatah party's defeat by Hamas in the 2006 parliamentary elections. At the request of President Mahmoud Abbas, Qurei remained in office in a caretaker capacity until being replaced by Ismail Haniyeh on 29 March 2006.