The new president will be chosen by members of the federal and provincial assemblies. Musharraf resigned on Monday in the face of impeachment hearings.
"Presidential elections will take place on September 6," said Commission Secretary Kanwar Dilshad. "Documents for the nomination of candidates will be accepted until August 26."
The procedure to elect a leader for the Asian nuclear power will take around five hours and the identity of the new president will be made public on the day of the polls.
Musharraf's resignation stoked fears that the populous Asian state could slide further into instability and chaos, and on Thursday Taliban militants carried out their deadliest attack yet against the country's military, killing over 60 people in twin suicide bombings at Pakistan's main munitions factory.
The attack took place in the town of Wah, on the country's border with war-torn Afghanistan.
Pakistan's current ruling collation is split over its candidate for the elections. The coalition's leading party, the Pakistan People's Party, favors its leader, Asif Ali Zardari, the widower of the late former prime minister, Benazir Bhutto. The Pakistan Muslim League, led by another former prime minister, Nawaz Sharif, looks likely to nominate its own candidate.
The coalition, which was elected in February, is also split over the issue of some 60 judges dismissed by Musharraf last year. Sharif is insisting on their reinstatement, and has pulled his ministers from the coalition Cabinet, warning that his party will quit the alliance altogether unless a decision is taken to return them to their posts on Friday.
Although the coalition would probably be able to survive such a move, it would undoubtedly be yet another blow to stability in the country and likely to cause its stock market to plunge further. Pakistan's stock market has fallen some 29% since the beginning of the year.
Talks were due to be held on Friday between senior officials from the parties to try to resolve the crisis.
Musharraf dismissed the judges last November during a state of emergency in order to prevent them from overturning his re-election as president.
