The 96-year-old, now rarely carries out public engagement outside of her royal residence but was joined by her youngest son the Earl of Wessex for the official visit on Tuesday.
Wearing a sunshine yellow outfit, the Queen arrived at 11.32am, stepping carefully from the transparent lift while holding a walking stick.
The visit comes just two weeks before her Platinum Jubilee celebratory weekend.
A Buckingham Palace spokeswoman said: “In a happy development, Her Majesty The Queen is attending today’s event to mark the completion of the Elizabeth line.
“Her Majesty was aware of the engagement and the organisers were informed of the possibility she may attend.”
The visit comes just days after she rallied to make a trip to the Windsor Horse Show on Friday and on Sunday as the guest of honour at the equestrian extravaganza A Gallop Through History near Windsor, the first major event of the Jubilee festivities.
Tuesday’s engagement is the Queen’s first one outside of the Windsor area since she attended the Duke of Edinburgh’s memorial service in Westminster Abbey seven weeks ago.
The Queen and Prince Edward were welcomed by the Prime Minister Boris Johnson and Mayor of London Sadiq Khan as well as Transport for London commissioner Andy Byford.
The group met staff who have been key to the project and run the railway, including train drivers, station staff and apprentices.
The Elizabeth line, named in honour of the Queen, will open to passengers on May 24.