It comes after the week-long window was cut to four days.
The changes will come into effect on June 13 and mean those travelling on long weekends will be unable to check in to all their flights at once unless they pay an extra fee.
The Dublin-based carrier is offering those affected and unhappy with the changes a full refund by May 19.
Travellers will still have up to two hours before the flight to check in.
A spokesperson told Sun Online Travel: “Online check-in (for those customers who don’t choose reserved seats) will be available from 48 hours to two hours pre-departure for all flights from June 13.
“This is more than double the 24 hour check-in period operated by British Airways, Lufthansa, Norwegian and Iberia. This will give reserve seat customers more time to select their preferred seats prior to departure.”