"Today I lost those who for 24 years I called...my family," said Enes Kanter of the Oklahoma City Thunder.
Turkish President Recep Tayyip Erdogan blames Mr Gulen for inciting a failed coup last month and is seeking the cleric's extradition to Turkey.
Mr Gulen, who has a large following, denies being involved in the coup.
Kanter's father, Mehmet, disowned his son in a letter published on Monday by Sabah, a pro-government newspaper.
Mehmet Kanter wrote his son had been "hypnotised" by the Gulen movement.
"With a feeling of shame I apologise to our president and the Turkish people for having such a son," the letter said.
Q&A on the Gulen movement
Mr Gulen is regarded by followers as a spiritual leader and sometimes described as Turkey's second most powerful man.
Enes Kanter has been a vocal supporter of Mr Gulen on Twitter.
The movement - known in Turkey as Hizmet, or service - runs schools all over Turkey and around the world, including in Turkic former Soviet republics, Muslim countries such as Pakistan and Western nations including Romania and the US, where it runs more than 100 schools.
In May 2016, the Turkish government formally declared the Gulen movement a terrorist organisation.
After the failed coup, suspected Gulen supporters in Turkey were purged in a wave of arrests.
Western nations have been critical of the government's response to the coup. US officials have said they will extradite Mr Gulen only if Turkey provides evidence.
An American basketball player has cut ties with his Turkish family over his support for Pennsylvania-based preacher Fethullah Gulen.