Afghan Voice Agency (AVA_Monitoring, Khan was arrested in May by Pakistani authorities in connection with a corruption case, which sparked deadly unrest across the country. He was released on bail within days.
It was not immediately clear which charge the Election Commission's order related to and whether police would act on the warrant. Geo did not disclose its source.
Khan has faced a multitude of charges in different institutions and courts since his ouster, including graft, murder and sedition.
The latest in the string of cases came last week when Pakistan's interior minister said the government would open criminal proceedings against Khan on charges of exposing official secrets, in relation to diplomatic correspondence between Washington and Islamabad.