Ryanair tweeted: 'Despite the regrettable and unjustified strike action taking place in five of our 37 markets, over 2,000 Ryanair flights will operate as normal, carrying nearly 400,000 passengers across Europe'.
A total of around 400 flights Europewide have been cancelled due to the strike action, AFP reported - equating to around 55,000 passengers.
The airline has cancelled its morning flights between Budapest and Berlin as well as Nuremberg and its evening flight to Brussels South Charleroi Airport, according to the flight information system of Liszt Ferenc International Airport operator Budapest Airport.
Under the agreement, the British Airline Pilots' Association (Balpa) was recognised as the sole trade union representing all of Ryanair's 600 employed pilots based in the UK.
Over 2,000 Ryanair flights, representing 85 percent of schedule, will operate as normal, carrying nearly 400,000 customers across Europe.
Ryanair was forced to cancel almost 400 flights on Friday because of pilot strikes in some of its biggest markets.
"Pilots are not nomads who put up tents wherever Ryanair wants to operate", union negotiator Ingolf Schumacher said.
Ryanair said: "If your flight is cancelled there are two options available to you to choose from".
Belgian consumer protection group Test Achats meanwhile announced it was taking Ryanair to the European Court of Justice to demand compensation for affected passengers.
In response to the latest strike announcement in Germany, chief marketing officer Kenny Jacobs said: "We regret the decision of the VC to go ahead with this unnecessary strike action given that we sent through a revised proposal on a collective labour agreement (on Friday, 3 August) and stated our intention to work towards achieving a CLA together".
Nearly 400 flights have been cancelled today, affecting more than 55,000 passengers.
It accused Ryanair of "categorically" ruling out higher personnel costs for cockpit crew, leaving no room for a compromise. "The responsibility lies with Ryanair management", Cockpit president Martin Locher told a press conference at Frankfurt airport today.
The strikes follow a move by the low-priced carrier to recognise unions first time in its 30-year history late last year.
The airline has already been hit with strikes by flight attendants in Spain, Portugal and Belgium. "Ryanair alone is to blame for the escalation of the situation which has now occurred".
Another key complaint of workers based in countries other than Ireland is the fact that Ryanair employs them under Irish legislation, arguing most of its employees work on board Irish planes.
Staff is holding a 24-hour walkout over pay and conditions.