Security and health concerns had prevented him from attending earlier hearings, and he has been in hospital for more than a month.
Mr Musharraf is accused of unlawfully suspending the constitution and instituting emergency rule in 2007.
He is the first former military ruler to be tried in Pakistan, and faces the death penalty if found guilty.
The 70-year-old arrived for the hearing at the National Library in Islamabad in a heavily protected convoy.
Mr Musharraf’s lawyer, Ahmed Raza Qasuri, told the BBC that the ex-leader was only in court for 20 minutes.
Mr Musharraf’s legal team argue that he should be tried in a military court, not a civilian one.
The BBC’s Shahzeb Jillani in Pakistan says the court has not charged Mr Musharraf and will decide on Friday whether it has the jurisdiction to try a former army chief.
He also faces further charges of murder and restricting the judiciary.
Mr Musharraf says all the accusations against him are politically motivated.
As president from 2001 to 2008, he was one of Pakistan’s longest-serving rulers.
He was in self-imposed exile, mostly in the UK , from 2008 onwards, before returning to Pakistan in March 2013.