The former army chief returned last month after nearly four years of self-imposed exile to contest a May 11 general election despite the possibility of arrest on various charges and death threats from the Pakistani Taliban.
The Election Commission barred Musharraf from the polls in Kasur in Punjab province because of court cases against him, commission officials said. He could also face disqualification in the three other constituencies where he plans to run.
The officials, who declined to be identified, also said the decision was based on a clause in the constitution which requires candidates to be of good character and the fact that he had not declared all of his assets.
"Musharraf has been disqualified under articles 62 and 63 of the constitution, among other reasons," an election commission official said, referring to clauses that require a candidate to be "of good character", among other things.
Neither Musharraf nor a spokesman for him were available for comment.
Musharraf faces charges of failing to provide adequate security to former prime minister Benazir Bhutto before her assassination in 2007.
He also faces accusations in connection with the death of a separatist leader in the southwestern province of Baluchistan. He denies any wrongdoing.
A petition which will be heard by the Supreme Court on Monday accuses Musharraf of committing treason when he sacked senior judges and declared emergency rule while in power.
The current chief justice, Iftikhar Chaudhry, was embroiled in a confrontation with Musharraf, who removed him from office in 2007 after he opposed plans to extend the general's term in office. He was later reinstated.
Musharraf had hoped to compete in the election. Former Prime Minister Nawaz Sharif, the man Musharraf ousted in a coup in 1999, is seen as the front runner.
Musharraf, a former commando, has been far removed from Pakistan's troubles during his exile in London and Dubai, where he lived in a posh part of the Gulf Arab emirate.
Pakistan's military has ruled the nation for more than half of its 66-year history, through coups and from behind the scenes. It sets foreign and security policy, even when civilian administrations are in power.
But current commanders have meddled far less in politics than during Musharraf's era, preferring instead to let civilian governments take the heat for the country's failures.