The man, from the city who was arrested by detectives yesterday and taken to Musgrave Serious Crime Suite, is also charged with possession of a firearm with intent to endanger life and professing to be a member of a proscribed organisation.
He will appear at Derry Magistrates Court on Thursday, 13 February.
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.”
The 52 year old man is one of a number of individuals subject to this ongoing murder investigation.
The N=w IRA later admitted the murder of Ms McKee.