Pervez Musharraf was present at the Islamabad High Court when the judges issued the order. He had been seeking to extend bail in the case.
Police present at the court did not arrest the former general when the order was made.
Pervez Musharraf immediately left the court and drove away escorted by his security detail.
Despite an unwritten judicial convention discouraging police arrests on court premises, suspects are normally handcuffed in court.
Pervez Musharraf can file an appeal against this court order in Pakistan’s Supreme Court.
The former leader returned from years of self-imposed exile last month hoping to lead his All Pakistan Muslim League (APML) party into the general election next month.
But earlier this week his candidacy was rejected in Chitral, one of four seats he had applied to contest. He had already failed in an attempt to stand in three other seats. His legal team plan to appeal against that decision.
Pervez Musharraf is embroiled in a series of legal battles and has been attempting to stave off arrest ever since he returned, as well as an attempt to try him for treason. The Pakistani Taliban have also vowed to assassinate the former president, who seized power in a 1999 coup.
He is facing a number of charges related to his time in office with court proceedings over the killing of Benazir Bhutto in 2007 and a tribal leader from Balochistan.
He has described all the cases against him as “baseless” and politically motivated.
This is the first arrest warrant issued for the former ruler since his return to Pakistan.
Pervez Musharraf has already been barred by a court from leaving the country.
Many analysts believe that the authorities would not welcome his arrest at such a politically sensitive time.
Pakistan’s powerful military, of which he was the head until 2007, has not intervened to prevent his political fall.
But while his future appears increasingly bleak, few believe the military would allow a former chief to be thrown in jail or assassinated by militants.
Unconfirmed reports suggest Pervez Musharraf could still be arrested and detained at his property close to Islamabad, where he went after leaving court.
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