Paul McIntyre, from Derry, is accused of killing Ms McKee, 29, who was shot dead by dissident republicans while observing a riot in Creggan in April last year.
Supporters of the 52-year-old holding placards saying he is a “political hostage” and a “British scapegoat” scuffled with up to 40 police officers as they refused to move from the entrance to Derry Magistrates’ Court on Thursday.
There were loud cheers as McIntyre was brought out of a Range Rover and taken into the court building at Bishop Street.
Ms McKee was standing near a police landrover when she was hit by a bullet to the head fired by a masked gunman towards officers.
The writer was living in the city with her partner, Sara Canning, who also arrived at court on Thursday morning.
Ms Mckee’s sister Nichola Corner was among several people in the public gallery wearing T shirts emblazoned with her picture with the words “Speak out for Lyra” emblazoned on the front.
In a statement on Wednesday, Detective Superintendent Jason Murphy said: “I have always said a number of individuals were involved with the gunman on the night Lyra was killed, and while today is significant for the investigation the quest for the evidence to bring the gunman to justice remains active and ongoing.”Ms McKee was a gay rights activist and an articulate advocate of a new and more tolerant Northern Ireland and part of the generation which reached adulthood during peace time.
Her funeral was attended by then British prime minister Theresa May, Irish Taoiseach Leo Varadkar and Irish President Michael D Higgins at St Anne’s Cathedral in Belfast.
Catholic priest Fr Martin Magill received a standing ovation when he asked why it took her death to unite politicians.
Days later the British and Irish governments announced a new talks process aimed at restoring devolution.
Powersharing was resurrected last month and the first same-sex marriage in Northern Ireland took place this week.
McIntyre is also charged with possession of a firearm with intent to endanger life and belonging to or professing to be a member of a proscribed organisation.
His address was given in court as Kinnego Park, Derry.
Inside the Bishop Street building, the court heard that evidence in the case included footage from music television channel MTV, as an MTV crew had been in the city filming that day, as well as mobile footage from members of the public.
Mr McIntryre’s defence solicitor said his client faced allegations that he was seen “picking up casings” that had come from a gun after it was fired by another male who Mr McIntyre was standing behind.
He added that there was “scant” evidence against him.
Mr McIntyre spoke only to confirm his name and address.
District Judge Barney McElholm said: “A woman with her entire life ahead of her, a very promising life, was murdered needlessly and pointlessly, like all the other murders in this country.
“It is very important that the murderers of Lyra McKee are brought to justice if this can be done, but we need to get the right people.”
The judge said that protesters’ behaviour, blocking the court’s entrance and “threatening journalists”, was doing Paul McIntyre “no favours whatsoever”.
Mr McIntyre has been remanded in custody until Thursday, February 27.