Shortly after Musharraf's seizing of the government in 1999, several Pakistanis filed court petitions challenging his assumption of power. Musharraf had always claimed his intention was to institute democracy in Pakistan. But in the face of the threat from the court, he issued an order that required all judges to take new oaths of office and agree not to make any rulings against the military. Many judges resigned instead, calling the move unconstitutional. The Pakistani Supreme Court asked Musharraf to hold national elections by October 12, 2002. To ensure his continued control, Musharraf held a referendum on April 30, 2002, to extend his term of office another five years after the October elections. Musharraf's government claimed an 80 percent turnout in favor of the referendum, but election officials reported some irregularities—for which Musharraf apologized—and the decision to hold October elections stood.

In October 2002, national elections were held, and the pro-Musharraf Pakistan Muslim League won a plurality in the Parliament. But opposition parties and coalitions formed against Musharraf, and the Parliament was virtually paralyzed for over a year. In November 2003, Musharraf agreed to hand certain powers over to the newly elected Parliament. The National Assembly elected Mir Zafarullah Khan Jamali as prime minister. In December, Musharraf made a deal with a coalition of six Islamic parties to leave the Army by the end of December 2004. In exchange, the Parliament passed the 17th Amendment, which retroactively legalized Musharraf's 1999 coup. But militant extremists continued to criticize his moderate policies at home. They often openly defied his directives until he brought in the army to quell the rebellions. In late 2004, he went back on his agreement to leave the Army, stating that the country was in too much turmoil for him to relinquish power, and pro-Musharraf legislators passed a bill allowing Musharraf to hold both the chief-of-Army and head-of-state positions.