Jinnah became the first Governor-General of Pakistan and president of its constituent assembly.

The office of Governor-General was ceremonial, but Jinnah also assumed the lead of government. The first months of Pakistan's independence were absorbed in ending the intense violence that had arisen in the wake of acrimony between Hindus and Muslims. Jinnah agreed with Indian leaders to organise a swift and secure exchange of populations in the Punjab and Bengal. He visited the border regions with Indian leaders to calm people and encourage peace, and organised large-scale refugee camps. Despite these efforts, estimates on the death toll vary from around two hundred thousand, to over a million people. The estimated number of refugees in both countries exceeds 15 million.The then capital city of Karachi saw an explosive increase in its population owing to the large encampments of refugees, which personally affected and depressed Jinnah.

Inaugurating the assembly on August 11, 1947, Jinnah spoke of an inclusive and pluralist democracy promising equal rights for all citizens regardless of religion, caste or creed. This address is a cause of much debate in Pakistan as, on its basis, many claim that Jinnah wanted a secular state while supporters of Islamic Pakistan assert that this speech is being taken out of context when compared to other speeches by him.

On October 11, 1947, in an address to Civil, Naval, Military and Air Force Officers of Pakistan Government, Karachi, he said:

We should have a State in which we could live and breathe as free men and which we could develop according to our own lights and culture and where principles of Islamic social justice could find free play.

On February 21, 1948, in an address to the officers and men of the 5th Heavy Ack Ack and 6th Light Ack Ack Regiments in Malir, Karachi, he said:

You have to stand guard over the development and maintenance of Islamic democracy, Islamic social justice and the equality of manhood in your own native soil. With faith, discipline and selfless devotion to duty, there is nothing worthwhile that you cannot achieve.

In his first visit to East Pakistan, under the advice of local party leaders, Jinnah stressed that Urdu alone should be the national language; a policy that was strongly opposed by the Bengali people of East Pakistan (now Bangladesh). This opposition grew after he controversially described Bengali as the language of Hindus.

Jinnah authorised force to achieve the annexation of the princely state of Kalat and suppress the insurgency in Baluchistan. He controversially accepted the accession of Junagadh—a Hindu-majority state with a Muslim ruler located in the Saurashtra peninsula, some 400 kilometres (250 mi) southeast of Pakistan—but this was annulled by Indian intervention. It is unclear if Jinnah planned or knew of the tribal invasion from Pakistan into the kingdom of Jammu and Kashmir in October 1947, but he did send his private secretary Khurshid Ahmed to observe developments in Kashmir. When informed of Kashmir's accession to India, Jinnah deemed the accession illegitimate and ordered the Pakistani army to enter Kashmir. However, Gen. Auchinleck, the supreme commander of all British officers informed Jinnah that while India had the right to send troops to Kashmir, which had acceded to it, Pakistan did not. If Jinnah persisted, Auchinleck would remove all British officers from both sides. As Pakistan had a greater proportion of Britons holding senior command, Jinnah cancelled his order, but protested to the United Nations to intercede.

This is not a full account of Quaid's role as Governor General. You may consult some quality books on this topic.

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“There is no God but You (Allah Almighty), You are far exalted and above all weaknesses, and I was indeed the wrongdoer”. AL-QURAN