A police squad and commandos reached the AFIC early in the morning to escort Musharraf to the court.
For the former army strongman's security, 3,000 police and Rangers personnel were deployed on the routes.
Musharraf has been charged with high treason for suspending the constitution when he declared emergency rule in 2007.
He took over in a bloodless coup when he dismissed the government of then prime minister Nawaz Sharif in 1999.
Musharraf, who resigned in 2008 as president and went into exile, returned to Pakistan in March last year to run in the parliamentary elections.
However, a court disqualified him from competing in the general elections in May.
