An election tribunal disqualified Pervez Musharraf from running in Chitral in the north-west. Earlier, he failed in an attempt to stand in three other seats.
Pervez Musharraf’s lawyer says he plans to file an appeal with the Supreme Court.
Meanwhile, at least four people were killed in an attack on a convoy of the main opposition PML-N party in the south-western province of Balochistan.
Pervez Musharraf returned from self-imposed exile in Dubai last month saying he wanted to save Pakistan.
The former military ruler is already embroiled in a series of legal battles attempting to stave off arrest, and a bid to try him for treason.
In addition to his legal and political problems, Pervez Musharraf is facing a security threat from the Pakistani Taliban, who have vowed to target him with a squad of suicide bombers.
There was no immediate claim for the attack in Balochistan. Correspondents say the area has no Taliban presence and is known to be a hotbed of separatist rebel activity.
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