Musharraf's presidential term ends on November 15. His nomination was filed by Prime Minister Shaukat Aziz.
The deadline for nominations is the end of September, with the official candidate list to be made public on October 1.
Security in the Pakistani capital of Islamabad is being tightened in response to opposition protests planned for Thursday. The opposition has announced its intention to carry out a "historical protest" against Musharraf's re-election bid.
There is currently a high police and military presence in the capital, and armored vehicles have been deployed. The Supreme Court and the Election Commission are also under the protection of security forces, and all roads leading to Islamabad have been blocked.
The Supreme Court is currently considering petitions from opposition parties claiming that Musharraf, as the armed forces commander in chief, is not entitled to run for president.
Musharraf said earlier he would quit the army if he won another presidential term, but would probably keep his post if not re-elected. Under the Pakistani constitution, the Electoral College is made up of members of the National Assembly, Senate and provincial assemblies. To win, Musharraf needs a majority vote, which is assured by his Pakistan Muslim League party.
The opposition parties have vowed to boycott the election and promised to resign from parliament and assemblies of all four provinces if Musharraf is re-elected.
The presidential election is to be followed by the parliamentary.
General Pervez Musharraf seized power in a bloodless military coup in 1999. After the 2002 parliamentary election, Musharraf retained his presidential and military titles, as well as the right to dissolve parliament and dismiss the government.
Two exiled former prime ministers - Nawaz Sharif and Benazir Bhutto - have already expressed their intention to run for seats in the new parliament.
Bhutto, who leads Pakistan People's party, earlier said she was planning to return home on October 18, after more than eight years of self-imposed exile.
Sharif returned to Pakistan on September 10, but was deported to Saudi Arabia shortly after his plane had touched down at Islamabad airport.
