Additional Sessions Judge Wajid Ali Khan rejected pleas by the former president's counsel to grant him exemption from appearing in court.
The court issued a bailable arrest warrant and ordered 71-year-old Musharraf to appear in person during the next hearing on April 2.
Police had registered a case against Musharraf in 2013 over the alleged murder of Rasheed who was killed in an army operation to flush out militants holed up in Islamabad's Lal Masjid in 2007.
The ex-army chief has refused to appear in court on health and security grounds. It is not clear whether he will appear at the next hearing.
Musharraf faces a string of court cases dating back to his 1999-2008 rule, including treason charges over his imposition of emergency rule in 2007 and involvement in the killing of Baloch nationalist leader Nawab Akbar Bugti in 2006 and the assassination of former Prime Minister Benazir Bhutto in 2007.
He has also been charged in the judges' detention case.
Musharraf came to power in a bloodless coup in 1999, deposing then-Prime Minister Nawaz Sharif.
Facing impeachment following elections in 2008, Musharraf resigned as president and went into self-exile in Dubai.
He returned to Pakistan after five years of self-exile to contest the general elections in 2013 which he lost.

Latest News from World News Desk