In May 2016, a man with a conviction for murder climbed over the wall and walked for about 10 minutes around the grounds of the palace before being arrested.
The 22-year-old man is believed to have scaled the front gates of the palace entrance by The Mall.
Buckingham Palace declined to comment, and said it is a matter for the police.
Her Majesty The Queen was in residence at the time as she had just returned from a visit to Cambridge.
An intruder was on the loose at Buckingham Palace at 2am this morning while the Queen slept just metres away.
The 22-year-old was held on suspicion of trespass at around 02:00 BST on Wednesday by specialist royal officers, the Metropolitan Police Service said.
After being arrested, the man was found not to be armed and remains at a central London police station.
The most famous came in 1982, when 33-year-old unemployed British man Michael Fagan broke into Buckingham Palace and entered the Queen's bedroom.
A royal source alleged that the intruder was trying to replicate Michael Fagan, who cunningly broke into the monarch's bedroom 37 years ago.More news: Former Tennessee Titans DL Albert Hayneswroth 'in Dire Need of a Kidney'
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The Duke of Edinburgh, who has been based on the Queen's Sandringham Estate in Norfolk since his retirement in 2017, was not at Buckingham Palace.
The source says the intruder was detained under the mental health act.
"How is it possible all these years later that someone can climb the fence and get right inside the grounds without being stopped immediately? It's very odd given the infamous Fagan business almost 37 years ago", the source says. "The Queen's safety should be paramount".
It wasn't until four minutes later that he was apprehended by police, reports The Sun.
Another source added: "Everyone knows the Queen was there because the Royal Standard was flying".
No members of the royal family were at the palace at the time, and the man, who was found shortly before 10.30pm "in an area now open to the public during the day", was arrested for burglary, trespass and criminal damage.
She then telephoned the switchboard but the operator thought it was another member of staff playing a joke and replied: "Yes, dear, you're the Queen, we'll send someone up!"
As he sat on the end of the Queen's bed, Fagan smashed a large glass ashtray and threatened to slash his wrists.
The Queen's aide Paul Whybrew was able to guide him into police custody.