Customers affected by the cancellations should have been notified by email and SMS text message yesterday and advised of their options of a refund, free move onto the next available flight or reroute.
From January this year, the Cockpit Union is negotiating with the leadership of the Irish airline, achieving the conclusion of the first tariff agreements with Ryanair and salary increases.
Walkouts called by German and Belgian unions accounted for numerous cancelations, with strikes also called in Sweden and Ireland.
"Ryanair alone is responsible for the escalation we are now seeing", Cockpit president Martin Locher told a news conference on Wednesday.
It also sought legal action to prevent Dutch pilots going on strike, this was rejected by Dutch courts. But the court ruled in the pilots' favor on Thursday afternoon.
However, Judge Theo Roell said this evening: "The strike may go ahead".
There are nine flights between the Netherlands and Spain on Friday, but only the Eindhoven-Reus and Eindhoven-Valencia routes are operated by Dutch employees.
Ryanair urged the unions to continue negotiations instead of calling any further strike action.
Ryanair pilots in several European countries staged a strike over work conditions on Friday that prompted the budget carrier to cancel 400 flights.
Over 2,000 Ryanair flights, representing 85 percent of schedule, will operate as normal, carrying nearly 400,000 customers across Europe.
The Irish airline, Europe's largest low-priced carrier, averted widespread strikes before Christmas by agreeing to recognise unions for the first time in its 30-year history.
Since then, however, it has struggled to reach agreements.
The union won the case, but Ryanair later said that all of its flights there will run on schedule.
Disgruntled pilots from the five countries will walkout for 24-hours today, throwing holiday plans into chaos in the height of the summer season.
Staff claim this creates huge insecurity for them, blocking their access to state benefits in their country.
Speaking at a Frankfurt press conference, Jacobs said German pilots enjoyed "excellent working conditions" with an average salary of around 150,000 euros ($173,000) a year, more than their peers at low-priced rival Eurowings.
Ryanair said it had informed passengers affected by the cancellations.