Patrick Gillespie, from Craigvar Street, Glasgow, appeared before the Special Criminal Court in Dublin more than 10 years on from the killing of the top Sinn Fein official.
Donaldson, 55, a close colleague of party president Gerry Adams, was shot dead at an isolated cottage near Glenties in Co Donegal in April 2006.
Gillespie, who was arrested in the county on Tuesday, was remanded in custody by the non-jury court.
He sat in the court during the brief hearing wearing tinted glasses, a green t-shirt and a black jacket.
The three judges, Cormac Dunne, Alison Lindsay and presiding judge Paul Butler, heard Gillespie is charged with having information between between April 3 2006 and July 26 2016 regarding the involvement of another person in the Donaldson murder.
Detective Sergeant Barry Doyle gave details of the arrest and said the accused made no reply when the charges were put to him.
Gillespie’s lawyer, Michael Gillespie LLB, disputed the principle address in Scotland that was given for his client and said he lived at Cronashallog, Dungloe, Co Donegal.
The Det Sgt told the court: “I do not accept that. His main residence is in Glasgow.
“I accept that he makes trips to Dungloe.”
Det Sgt Boyle told the court that he met Gillespie on Main Street, Dungloe, on Tuesday July 27 and arrested him later at 10.25pm.
The court heard that the alleged offence was contrary to section nine of Ireland’s Offences Against the State Act 1998.
Mr Gillespie LLB told the court his client would apply for bail, legal aid and “whatever other applications” that would be advised.
Judge Butler refused an application from the solicitor for the charge to be struck out over a procedural matter in the arrest.
Mr Donaldson had been living in a remote area of Donegal following his exposure as an MI5 agent a year before his death.
Dissident republican group the Real IRA claimed responsibility for the murder in 2008, but the circumstances surrounding Mr Donaldson’s outing as a British agent and subsequent assassination have long been shrouded in mystery.
A long-delayed inquest into the shooting has been adjourned almost 20 times.
Gardai have repeatedly urged the coroner to postpone the probe, citing concerns it might compromise their criminal investigation.
In 2014, the Garda made a mutual assistance request to a police force outside the Irish Republic in a bid to gain what it described as potentially “significant” evidential material.
That material was secured in March this year.
Gillespie was one of two men arrested on Tuesday in Donegal.
The second man, aged in his 40s, was released without charge and a file is being prepared for the Director of Public Prosecutions.