The 96-year-old monarch, who now rarely carries out public engagements outside of her royal residences, was joining her youngest son, Prince Edward for the official visit on Tuesday.
Her attendance was not publicly announced in advance, with the head of state facing ongoing mobility problems, but organisers were told there was a possibility she might be able to attend.
The nation’s longest reigning head of state is just over two weeks away from her Platinum Jubilee celebratory weekend starting on June 3rd.
“Her Majesty was aware of the engagement and the organisers were informed of the possibility she may attend.”
The Queen smiled warmly as she met Crossrail and Elizabeth line workers and walked slowly as she made her way around the station concourse.
Elizabeth line customer experience assistant Kofi Duah said he was “thrilled” to present an Oyster card to the Queen and show her how it could be topped up on a machine.
Mr Duah told the PA news agency: “I gave her an Oyster card and told her she can tap it on the yellow reader.
“I showed her the current balance and how to top up the Oyster.
“She said ‘Where can I use it?’.
“I said ‘You can use it across our line, so from Paddington to Abbey Wood.
“She said ‘Oh nice, splendid’.”
The Queen rallied to make a trip to the Windsor Horse Show on Friday and on Sunday was the guest of honour at the equestrian extravaganza A Gallop Through History near Windsor, the first major event of the Jubilee festivities.
But 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.
Unveiling a plaque stating that she had “officially opened” the Elizabeth line, the monarch spent 10 minutes in the station before departing in a lift, escorted by her son Edward.
The Queen and Edward were being welcomed by Prime Minister Boris Johnson, Mayor of London Sadiq Khan and Transport for London commissioner Andy Byford.
They were meeting staff who have been key to the project and who will 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.
Crossrail, the project to build the new east-west railway, was delayed and over budget due to numerous issues including construction difficulties and complications installing signalling systems.
It was due to be completed in December 2018 and was set a budget of £14.8 billion in 2010.
The total cost has been estimated at £18.9 billion, including £5.1 billion from the Government.
The Elizabeth line will boost capacity and will cut journey times for travel across the capital.