Mick Kendrick was at the station at around 11.15am on Monday, June 27, when he noticed a large police presence around.
He guessed that it might be a high-ranking royal, but was still surprised when he spotted the monarch.
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As she got off the train, passengers in the station cheered. Mr Kendrick said that one older lady started crying, and told him she felt she would never get to see this again.
“It was totally out of the blue”, he said.
“I had quite a special feeling, because the chances of seeing her again are probably slim.”
The 96-year-old monarch, who has cut back on public engagements due to mobility issues, was symbolically offered the keys to the city by Edinburgh Lord Provost Robert Aldridge.