The Metropolitan Police Service says the 22-year-old man was arrested on suspicion of trespassing early Wednesday by members of its royalty protection unit.
The intruder was not carrying any weapons and the incident is not being treated as terror-related, according to Scotland Yard.
It was nearly 37 years to the day from when Michael Fagan broke into Buckingham Palace and made it into The Queen's bedroom in 1982.
The Sun newspaper reported it had taken four minutes for officers to detain him and in the meantime he had banged on the doors of the 93-year-old queen's home while she was asleep inside.
She was reportedly the only senior royal sleeping in the household at the time.
According to ITV reporter Jonathan Swain, the man was able to climb the gates and bypass heat sensors, CCTV and armed guards to gain access to the grounds of the palace. Terrifyingly, a 33-year-old decorator called Michael Fagan entered her bedroom in July 1982 at 7.15 am.
Our royal insider revealed: "There was an intruder at the Palace while the Queen lay sleeping in her bedroom and he was on the loose for a good few minutes before the cops arrested him".
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The unidentified interloper remains in custody at a central London Police station.
One source told the paper the intruder was "banging down the doors".
Buckingham Palace declined to comment, but royal insiders said the Queen is aware of the incident.
In a 1993 BBC interview, Fagan highlighted the lack of security saying: "I don't know how the hell I found her [the Queen]".
"We are all relieved that the doors were locked this time and he wasn't able to get inside where the Queen was".
The freaky conversation saw the 31-year-old schizophrenic tell the Queen about his family problems.
During the incident Fagan smashed a large glass ashtray and threatened to slash his wrists.
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