The Queen, 87, sported a pink outfit for the flight, teeming a pink and gold coat with a flowery headscarf and then travelled by car to the remote castle in the Highlands.
The sovereign will spend the first part of her holiday without her husband, the Duke of Edinburgh, who is still recovering from his abdominal surgery.
Following several weeks recuperating with the Queen at Windsor Castle Prince Philip moved to Sandringham, the royal family's Norfolk estate.
Having made good progress in his recovery the 92-year-old is expected to join his wife at Balmoral in August, according to royal sources.
It is also thought that the Duke and Duchess of Cambridge and their new baby boy, Prince George, will also travel up to Scotland to spend time with the Queen.
Before Kate Middleton gave birth to Briatin's future king on Monday 22 July the Queen had said that she hoped the baby arrived before she left London for Balmoral.
"I would very much like it to arrive because I'm going on holiday soon," said the Queen to a schoolgirl during a visit to Kendal in Cumbria last week.
In the coming month William and Kate may also take Prince George to Sandringham to meet the Duke of Edinburgh for the first time.
The couple and their newborn are currently at the Middleton's family home in Berkshire.