The Court of Appeal has ruled the case, involving two men - identified only as AB and CD - can go ahead despite a legal challenge by media organisations.
It followed an earlier ruling at the Old Bailey it could be heard secretly.
It is thought to be the first time a case has been held in private, the media excluded and the defendants anonymised.
Anthony Hudson, the counsel for the media groups in the failed challenge, said: "The Crown has sought and obtained an unprecedented order that the trial of two defendants charged with serious terrorism offences should take place entirely in private with the identity of both defendants withheld and a permanent prohibition on reporting what takes place during the trial and their identities."
Mr Hudson said the appeal raised important issues relating to the constitutional principle of open justice, but also the equally important principle of natural justice.
He added: "This case is a test of the court's commitment to that constitutional principle in the admittedly difficult and sensitive circumstances where the state seeks to have trials involving terrorism held in secret and relies, in support of that, on grounds of national security."