Julien Dupuis, 39, appeared in private on petition from custody to face a charge of breach of the peace at Edinburgh Sheriff Court.
Dupuis, whose address was given as Edinburgh, made no plea during the brief hearing and was remanded in custody.
The case was continued for further examination and he is expected to appear back in court within eight days.
The court appearance comes after bomb disposal specialists were called out to the Palace of Hoyroodhouse following an alert on Tuesday night.
It is believed staff members at the palace raised the alarm of a suspicious package – a rucksack – at around 8.50pm.
Following the incident a Police Scotland spokesperson said: “We were called to Holyrood Palace, Abbey Strand, Edinburgh, around 8.50pm on Tuesday, 23 March, following a report of a suspicious item.
“Following examination by Explosive Ordnance Disposal (EOD), it was made safe. There was no threat to the public.
“A 39-year-old man has been arrested and charged in connection with the incident and is due to appear at Edinburgh Sheriff Court on Thursday, 25 March.”