David Belmar, 44, was held at around 11.30am yesterday after reports police stopped a man who had entered through the north centre gate and was stopped by police.
A Scotland Yard spokesman said: "He will appear in custody at West London Magistrates' Court on Tuesday."
Buckingham Palace said the Queen was not in the building.
Last month, another security alert was sparked at the palace when a suspected burglar managed to get into the building after scaling a fence.
He was found at around 10.30pm on September 2 in a room that had been open to the public during the day. A second man was arrested outside the palace on suspicion of conspiracy to commit burglary.
Less than 48 hours later, two police officers confronted the Duke of York in the palace gardens.