In 1958 Ayub Khan had promised a speedy return to constitutional government. In February 1960, an eleven-member constitutional commission was established. The commission's recommendations for direct elections, strong legislative and judicial organs, free political parties, and defined limitations on presidential authority went against Ayub Khan's philosophy of government, so he ordered other committees to make revisions.

The 1962 constitution retained some aspects of the Islamic nature of the republic but omitted the word Islamic in its original version; amid protests, Ayub Khan added that word later. The president would be a Muslim, and the Advisory Council of Islamic Ideology and the Islamic Research Institute were established to assist the government in reconciling all legislation with the tenets of the Quran and the sunna. Their functions were advisory and their members appointed by the president, so the ulama had no real power base.

Ayub Khan sought to retain certain aspects of his dominant authority in the 1962 constitution, which ended the period of martial law. The document created a presidential system in which the traditional powers of the chief executive were augmented by control of the legislature, the power to issue ordinances, the right of appeal to referendum, protection from impeachment, control over the budget, and special emergency powers, which included the power to suspend civil rights. As the 1965 elections showed, the presidential system of government was opposed by those who equated constitutional government with parliamentary democracy. The 1962 constitution relaxed martial law limitations on personal freedom and made fundamental rights justiciable. The courts continued their traditional function of protecting the rights of individual citizens against encroachment by the government, but the government made it clear that the exercise of claims based on fundamental rights would not be permitted to nullify its previous progressive legislation on land reforms and family laws.

The National Assembly, consisting of 156 members (including six women) and elected by an electoral college of 80,000 Basic Democrats, was established as the federal legislature. Legislative powers were divided between the National Assembly and provincial legislative assemblies. The National Assembly was to hold sessions alternatively in Islamabad and Dhaka; the Supreme Court would also hold sessions in Dhaka. The ban on political parties was operational at the time of the first elections to the National Assembly and provincial legislative assemblies in January 1960, as was the prohibition on "EBDOed" politicians. Many of those elected were new and merged into factions formed on the basis of personal or provincial loyalties. Despite the ban, political parties functioned outside the legislative bodies as vehicles of criticism and formers of opinion. In late 1962, political parties were again legalized and factions crystallized into government and opposition groups. Ayub Khan combined fragments of the old Muslim League and created the Pakistan Muslim League (PML) as the official government party.

The presidential election of January 1965 resulted in a victory for Ayub Khan but also demonstrated the appeal of the opposition. Four political parties joined to form the Combined Opposition Parties (COP). These parties were the Council Muslim League, strongest in Punjab and Karachi; the Awami League, strongest in East Pakistan; the National Awami Party, strongest in the North-West Frontier Province, where it stood for dissolving the One Unit Plan; and the Jamaat-i-Islami, surprisingly supporting the candidacy of a woman. The COP nominated Fatima Jinnah (sister of the Quaid-i-Azam and known as Madar-i-Millet, the Mother of the Nation) their presidential candidate. The nine-point program put forward by the COP emphasized the restoration of parliamentary democracy. Ayub Khan won 63.3 percent of the electoral college vote. His majority was larger in West Pakistan (73.6 percent) than in East Pakistan (53.1 percent).

Data as of April 1994