A document circulating on Facebook listed 14 private schools in Denmark as being linked to Gulen and urged parents to "Save your children from Fethullah Gulen's terror organisation's schools", according to a translation from Turkish by broadcaster TV 2.
A total of 366 students had been pulled out of the schools after the summer break, the broadcaster said.
At the Hillerød Private School 35 kilometres northwest of Copenhagen, 45 out of around 180 students had left, according to its deputy head Jørgen Skaastrup.
Parents "do not dare let their children go to a school that Erdogan has labelled a terrorist school", Skaastrup told AFP.
While the parents he had spoken to had told him that "they know they are not being brain-washed", some had received threats from family members in Turkey and were afraid of not being able to travel there, or of having property confiscated, he said.
Gulen's Hizmet movement has affiliated schools around the world. Most of the Danish schools on the list "confirmed being inspired by Gulen's ideas... on education", but denied having any direct links to him or including his ideas in their teaching, according to TV 2.
Skaastrup said that "on a personal level there are of course teachers among the Turkish staff who are inspired by Gulen".
"It is in no way whatsoever included in the school's curriculum, goal or values," he added.
Gulen is accused of ordering the July 15 coup during which a group within the Turkish military tried to remove President Recep Tayyip Erdogan from power, a claim he strongly denies.
Tens of thousands of his alleged supporters have been detained or sacked in a sweeping post-coup purge that has worried Ankara's Western allies.