Travellers using the budget airline said they had been charged up to £21 to book a seat on their flight, in order to access their e-boarding pass.
Those who refused to pay the fee claimed that they were forced to queue for a paper pass at the airport.
But a spokesperson for Ryanair denied that the airline had introduced the charge, despite furious complaints from passengers on social media.
One passenger travelling from London to Belfast on Monday tweeted: “When and why did you start this carry on? I now have to QUEUE to collect my boarding pass at the airport.”
Another passenger said: “I just can't believe your new policy of not allowing passengers to create a boarding pass (mobile or print-out) unless they buy a seat, forcing them to join a check-in queue (30m or longer) to do so for no other reason for you to make a few quid. Scandalous.”
And another passenger posted a screenshot of their app after checking in, with a message reading: "Get your boarding pass now and avoid queueing at the airport by adding a seat".
They wrote alongside the image: "Charging for a mobile boarding pass? You are ridiculous."
Ryanair passengers are usually provided with their digital boarding pass for free via their app. There is a separate fee for travellers wishing to book a specific seat on the flight.
A spokesperson for Ryanair said in a statement: “There is no charge for a Ryanair digital boarding pass – ever.
"All Ryanair passengers can pay for a reserved seat if they so wish or if passengers wish to avoid this seat fee, they can select a randomly allocated seat entirely free of charge.”
Ryanair is known for its low fares but has also been criticised for its numerous add-on charges.
This includes a fee for putting luggage in the hold, booking a seat and requesting a seat with extra legroom.
Ryanair's CEO Michael O'Leary has defended the airline's hidden fees, saying they are essential in order to keep fares low.
Consumer rights expert Martyn James told the BBC that the new fee was likely a malfunction on Ryanair’s computer or booking systems.
“If this new charge is true, then it's something of a false economy for Ryanair, as they'll need an awful lot more staff on the check-in desks to print off all of those boarding passes," he said.
“However, this latest news story highlights a glaringly unfair scenario that's been allowed to continue for far too long. Passengers should not have to pay for reserving a 'standard' seat at all. Speedy boarding, more legroom, premium - fine. But you should not have to pay to sit next to a loved one."