The Cathedrals Express trip, operated by firm Steam Dreams, was due to run on Thursday but Network Rail decided it could not go ahead.
Steam Dreams chairman Marcus Robertson said: “We bring 500 people to York half a dozen times a year and they spend a lot of money in the city.
“This has probably cost the company between £10,000 and £20,000.”
Network Rail said it received the firm’s application less than four weeks before the journey was due to go ahead.
This made it a “tall order” to arrange as June and July are the busiest months of the year for planning charter excursions.