The last of the country's four provinces rejected his nomination papers on Tuesday, Dawn News reported.
The former military strongman's attorney said the rejections would be appealed to the High Court.
Musharraf's appeals of two of the provincial rejections have already been denied. An official in Islamabad said the former president's papers had been returned in that province because of objections that Musharraf had subverted the constitution and illegally arrested judges while he was the head of the country.
Another province said his nomination papers had been refused because he violated the constitution three times.
Musharraf recently returned to Pakistan after five years in exile with the announced intention of running for president, a position he held from 2001 to 2008.