The budget airline has announced that passengers will only have 48 hours to check in for their flight instead of the usual four days.
This 48-hour window will then close two hours before the flight's scheduled departure time.
However, passengers who have decided to pay for an assigned seat will still be able to check-in up to two months ahead of the flight.
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Passengers who miss this narrow window will have to pay Â£55 to check in at the airport or Â£25 for infants.
Ryanair has announced that any disgruntled passengers will be offered a full refund on their tickets by May 19 should they disagree with the new policy.
A spokesperson for Ryanair told The Mirror : "Standard (free) online check-in will be available from 48 hours to 2 hours pre-departure for all flights from 13th June onwards, in order to increase the choice and time available to customers who choose to pay for reserved seats.
"All Ryanair customers may buy a reserved seat online, both on the Ryanair.com website and mobile app from the time of booking up to two hours pre-departure and these customers can check in online anytime they so wish between 60 days and up to two hours before the scheduled departure time of their flight.
"All affected customers booked to travel from 13th June have been contacted by email and those who do not wish to accept this check-in policy change can cancel and request a full refund within 5 days (of this 14th May notification) after which the change will be regarded as implicitly accepted."
Passengers can pay Â£4 to reserve a standard seat, Â£13 for priority boarding and Â£15 for priority seats with extra legroom.
Ryanair also introduced new hand luggage rules this year; ending their policy of allowing non-priority passengers two items of hand luggage.
Customers who have not purchased 'Priority & 2 Cabin Bags' will only be permitted to bring one small bag on board.
Their second 10kg bag will now be tagged at the gate and put into the hold without a charge.