Thomas Mair, 52, is accused of shooting and stabbing Ms Cox, 41, outside her constituency surgery in Birstall, near Leeds.
He is charged with murder, grievous bodily harm, possession of a firearm with intent to commit an indictable offence, and possession of an offensive weapon. He appeared at the Old Bailey via video link from top-security Belmarsh jail, amid a list of terror-related cases to be heard by Mr Justice Saunders.
The senior judge set a provisional timetable, with a trial to start on November 14.
Another hearing will take place on September 19, at the Old Bailey, with a plea hearing pencilled in on October 4. The trial will be heard before a High Court judge and is likely to be at the Old Bailey.
Grey-bearded Mair, from Birstall, whose case is being handled under the “terrorism protocol”, spoke only to confirm his name.
At a magistrates’ hearing last week, he gave it as “Death to traitors, freedom for Britain.”
Throughout, he sat with his head bowed, taking notes, and made no reaction as his lawyer, Cairns Nelson, QC, discussed his case with prosecutor, Mark Dawson, and the judge.
The preliminary hearing coincides with referendum day and comes the day after Mrs Cox’s widower, Brendan, and their two young children marked what would have been her 42nd birthday.
At the Commons event, they heard British Prime Minister, David Cameron, praise, Mrs Cox as “a voice of compassion, whose irrepressible spirit and boundless energy lit up the lives of all who knew her”.
Labour leader, Jeremy Corbyn, said that British society had lost “one of our very best”.