The shoe didn't hit Musharraf and the suspected perpetrator, one of several lawyers protesting against the former military ruler at his court appearance in Karachi, was led away by security officials, Dawn News reported.
Musharraf was seeking an extension of bail granted last week and related to charges in the 2007 killing of former Prime Minister Benazir Bhutto, his wholesale firing of judges in 2007 and the 2006 killing of Baloch leader Nawab Akbar Bugti.
Musharraf returned to Pakistan Sunday after four years in self-imposed exile.
Musharraf has called the cases against him "baseless" and politically motivated, the BBC reported.
He led Pakistan's military government from 1999 until 2008, when his supporters lost in parliamentary elections and he resigned under threat of impeachment. Musharraf has lived in London and Dubai since.