Metin Topuz, who liaised with the US Drug Enforcement Agency for the American mission, is accused of having links to US-based Muslim preacher Fethullah Gulen.
Ankara alleges that Gulen ordered a failed coup in 2016, but he denies the claims.
The Istanbul court, which accepted the prosecutor's indictment issued last month, ordered Topuz to remain in jail, state news agency Anadolu said.
He has been in custody since September 2017.
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Topuz's trial will begin on March 26 and the first hearing will last three days. He faces life in jail if found guilty.
The consulate employee is suspected of having contacts with former police officers and a prosecutor on the run accused of links with the Gulen movement, Anadolu reported.
The agency added that the indictment claimed Topuz had "very intense contacts" with former police chiefs involved in a 2013 probe into corruption allegations that affected government officials at the time.
Ankara has dismissed that investigation as an attempted "judicial coup" against the government by the Gulen movement.
Topuz had been at the centre of a visa row between Ankara and Washington in late 2017 after his arrest.
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Turkey-US relations have been strained in recent years over multiple issues including the US refusing to extradite Gulen.
There was also a bitter row last summer over the detention of an American pastor, but tensions eased after his release in October.
The court's decision comes a day after a judge in the southeastern city of Mardin convicted a former local employee of the US consulate in Adana, southern Turkey.
Hamza Ulucay was found guilty of helping outlawed Kurdish militants, and sentenced to four years and six months in jail.
But the Mardin court ruled he be released because of the time he had already served in jail since March 2017.
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