The former military ruler sent his resignation to the Election Commission as it was no longer possible for him to run the party from abroad, the party's new chairman Mohammad Amjad said.
Earlier this week, the poll body rejected Musharraf's nomination papers for NA-1 Chitral, after the Supreme Court withdrew its conditional approval for him to file nomination papers for the upcoming general election after he failed to appear before the court.
Mr Amjad, previously the general secretary of the party, has been elevated to the position of chairman. He will now be directing all party affairs and deciding APML's role in the elections, the Pakistani media reported.
Mr Musharraf founded APML in 2010. Despite the party announcing boycott of the 2013 election just days before the balloting, two of its candidates still contested and won two seats from Chitral.
The retired general was also barred from contesting the 2013 election due to cases registered against him.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.