The warrant came in the aftermath of Istanbul's chief public prosecutor request for Gulen’s arrest.
The court said that the arrest warrant had been issued within the scope of a probe against 80 suspects, who were all charged with "being members of an armed terrorist organization," "espionage," and "attempting to overthrow, or hinder the Turkish government."
The court also issued an arrest warrant for former police officer Emre Uslu on the same charges.
The "parallel state" is an alleged group of Turkish bureaucrats and senior officials embedded in the country's institutions, including the judiciary and the police, accused of trying to undermine the elected government.
A summary of proceedings was prepared about the "parallel state" operation in Istanbul and 12 other provinces in early February, authorities said Friday.
The document contained charges against 80 suspects, including Gulen, Uslu and a number of senior police officers.
Police had launched operations across Turkey on Feb. 8 in a move against the "parallel state," a movement allegedly formed by Gulen and his supporters, who deny all charges.
Following the Istanbul-based operation, a 1,758-page summary of proceedings was sent to Istanbul’s prosecution office.
The summary, for the first time, also included definitions of "terror and terrorism" and the "parallel state structure," in addition to the "Gulenist terror organization." The document also addressed the foundation, purpose, structuring, activities and strategy of the alleged organization.
Out of the 80 wanted suspects, 28 have been arrested. Gulen, who lives in the U.S., is the primary suspect in the probe, according to the summary.
The suspects are accused of illegal wiretapping, espionage, breaching private life, illegally recording personal data, forgery of official documents, establishing an illegal organization and attempting to overthrow the Turkish government.
This is Gulen's second arrest warrant. The first was one was issued on Dec. 19, 2014, following a police operation against senior media figures and police officers in 13 provinces across Turkey for allegedly being affiliated with the "parallel state".