Benazir Bhutto returned to power a second time in 1993 after the resignation of both the President Ghulam Ishaq Khan and the Prime Minister Nawaz Sharif on 18th July 1993.The resignation led to the announcement of fresh elections for the National and Provincial Assemblies. The elections were held on 6th October and 9th October 1993, respectively.

The elections were boycotted by the MQM. No party emerged with an absolute majority in the elections. As a result the PPP formed the new government with the help of alliances. Benazir Bhutto took oath as Prime Minister on 19th October 1993. Presidential election was held on November 13. Farooq Ahmed Khan Leghari the PPP candidate won by 274 to 168 votes against, the then acting President Wasim Sajjad. During her second tenure Benazir again faced trouble from the opposition, in autumn of 1994, Nawaz Sharif led a ‘train march’ from Karachi to Peshawar. This was followed by general strike on the 20th September. Two weeks later Nawaz Sharif called a ‘Wheel-jam’ strike on 11th October. The second tenure of Benazir Bhutto was however high lightened by the visit of the US first Lady Hillary Clinton and her daughter Chelsea in 1995. Hillary’s visit considerably changed Pakistan’s perceptions and highlighted Pakistan as a liberal, modern and forward-looking country. In April 1994 Benazir visited the US, and projected Pakistan’s stance on the US F-16 fighter planes .Her visit resulted in passing of the Brown Amendment by the US Senate, easing the restrictions on Pakistan on 21st September1995. It also helped in attracting foreign investors. On the domestic front she continued facing problems with MQM. In spite of all her political endeavors, a smooth relationship could not be established between the government and MQM.

Benazir Bhutto brother Mir Murtaza Bhutto was assassinated under mysterious circumstances on 20th September 1996.The high-profile killing of her brother harmed her the most.