So what's going on, when will it be fixed and how can you find out if your trip will be affected? You should get your money back within seven days or given an alternative flight.
Kenny Jacobs, chief marketing officer, said the company was "working hard to fix" the problem, after it announced a 2% reduction in scheduled flights until the end of October.
The carrier's current annual leave year runs from April to March, but it is now transitioning to a January to December schedule from 2018. The company is now in the cross-over period between these two holiday allowances and it has created some issues.
"The IAA requires us to move to a calendar year from January to December, starting in 2018".
Europe's largest airline by passenger numbers sent emails to the first affected passengers on Friday, giving them the choice of a refund or an alternative flight.
And a mother said her daughter's 21st birthday in Amsterdam had been ruined because her flight had been cancelled last minute - with hotels and tickets to museums unrefundable.
It has furnished a list of affected flights up until Wednesday, but so far Shannon flights aren't affected.
Bloomberg via Getty Images Up to 9,000 passengers a day could be affected by the cancellations
But he says they have only been given details of the cancellations up to Wednesday of this week so are "in the dark" after that.
If the airline cancels 40 flights per day for six weeks at a load factor of 90 percent, approximately 285,000 journeys would be affected.
Why are Ryanair cancelling flights?
How do I find out if my flight has been cancelled?
The company has informed all passengers whose flights have been cancelled, with a total of 56 flights cancelled today, 12 of which are departing from or arriving in Dublin.
Ryanair has the form on its website you need to fill-in.
Move quickly and try to reschedule your flight as soon as you find out yours is cancelled. Flights are operating as usual for customers who haven't received emails from the carrier.
Analysts at Dublin-based Goodbody Stockbrokers estimated the cancellations would cost the airline about €34.5 million, comprising €23.5 million in compensation, €6.3 million in lost fees, and €4.7 million in subsistence such as meals, drinks and accommodation.