The incident took place Monday night but was only revealed Saturday by Scotland Yard, and has raised questions about security at the royal residence.
The Metropolitan Police said one man scaled a fence outside the monarch's official London home and was found in one of the palace's state rooms at about 10 p.m. local time and apprehended. He has been charged with burglary, trespassing and criminal damage and was released on bail.
A second man was arrested outside the palace on suspicion of conspiracy to commit burglary. He has also been released on bail.
Queen Elizabeth was at Balmoral Castle in Scotland, where she often spends much of hersummer holiday. No other members of the royal family were in Buckingham Palace at the time, a spokesperson said.
The palace's state rooms, as well as various other parts of the 775-room building, are normally open to the public on summer days. It was not immediately clear, though, how the man would have found his way into the state rooms at night.
"A review of the incident is underway and the focus of that review will undoubtedly be security at Buckingham Palace," CBC News correspondent Dominic Valitis reported from London.
Security breaches at the palace are rare but not without precedent.
"In 2004, for example, a protester dressed as Batman and campaigning for fathers' rights in U.K. courts managed to slip past security and scaled the side of the palace, and he was up there for quite some time," Valitis noted.
"And another occasion, a tabloid newspaper journalist somehow managed to get through the vetting procedures after successfully applying for a job as a footman at the palace, and a series of exposés followed, apparently how the Queen likes to store breakfast cereal in Tupperware containers."
In one of the most famous break-ins, Michael Fagan, a father of four, managed to sneak into the Queen's private chambers in 1982 while she was still in bed. Elizabeth II spent 10 minutes chatting with the burglar before raising the alarm when he asked for a cigarette.