The court agreed an earlier request by prosecutors for the arrest notice but it remains to be seen if the United States will agree to extradite him to face trial on terrorism charges in Turkey.
The warrant was issued after the court earlier remanded in custody the head of a national TV network and three former police officers – all of whom are deemed linked to Mr Gulen – on terrorism charges.
Hidayet Karaca, head of Samanyolu TV, was arrested on charges of forming a terrorist group, after being detained with more than two dozen others in weekend raids on journalists, scriptwriters and police accused of plotting to overthrow Mr Erdogan.
The court however ordered the release of Ekrem Dumanli, the editor-in-chief of the Zaman daily, which has repeatedly accused the president of running a corrupt regime and who was arrested in the same raids last Sunday.
Both the Zaman newspaper and the STV channel are linked to Mr Gulen, a one-time ally of Erdogan whom the Turkish strongman has now vowed to crush without mercy.
Mr Dumanli defiantly told hundreds of supporters outside the court after his release that, “The press cannot be silenced, media will never succumb to intimidations.”
Seven other suspects in the case were ordered released by the court in Istanbul while three more – all ex-police officers – were also remanded in custody.
Mr Erdogan accuses his rival of running a “parallel state” and being behind sensational corruption allegations against his inner circle that broke on December 17 last year.
Mr Gulen, who is believed to have millions of followers in Turkey and runs private crammer schools around the world through his Hizmet (Service) group, has vehemently denied all the allegations against him.
Prosecutors asked the court for the warrant to arrest Mr Gulen for leading a “criminal” group acting against the “rules and laws in media, economy and bureaucracy”, the state Anatolia news agency reported.
According to a copy of the request published in Turkish media, he is charged with setting up and directing an “armed terrorist organisation” as well as using intimidation to deprive a person of their freedom.
The United States has so far paid little attention to repeated requests from Turkey for Mr Gulen’s extradition from his secluded compound in the state of Pennsylvania.
Jen Pskai, US State Department spokeswoman, said Washington did not comment on extradition cases.
The European Union had condemned the arrests as running contrary to European values but Mr Erdogan has refused to back down, telling the bloc to “mind their own business” in a row that risks damaging relations.
The arrests have also amplified concerns about media freedoms in Turkey under Mr Erdogan, who has dominated the country for 12 years and in August moved from the post of prime minister to president.