Many complained they had missed weddings or lost over a day of their holiday thanks to flights being cancelled, with waiting times of up to 10 hours in airports.
At least 400 Ryanair flights have been cancelled as a result, which has forced passengers who planned on travelling today to rebook or take different routes.
Ingolf Schumacher, pay negotiator at Germany's Vereinigung Cockpit (VC) union, said pilots had to be prepared for "a very long battle" and that it could take months to push through change at Europe's largest low-priced carrier.
Germany will be the country most affected by the strike with 250 flight cancellations across ten airports.
A Dutch court on Thursday evening rejected a case from Ryanair seeking to block pilots in the Netherlands from joining the strike, affecting about 22 flights.
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Customers have been notified and a majority of those affected moved to another Ryanair flight, the company said.
The hardest hit countries appeared to be Germany and Ireland, where flights between Berlin, Frankfurt, Hamburg and Dublin and airports in Britain were among those shelved.
But there have been protests ever since over the negotiating of collective labour agreements.
The unions want the contracts of Ryanair employees to be governed by the laws of the nation where they are based, not by Irish legislation.
But the "once in a lifetime experience" of being at her best friend Justine's wedding seems impossible now, after Ryanair cancelled her flight with two days' notice.
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Staff claim this creates huge insecurity for them, blocking their access to state benefits in their country.
Despite the walkouts, 85 per cent of its scheduled flights, more than 2,000, will operate as normal, Ryanair said.
The Spanish pilots' union - which represents around 500 of the 800 Ryanair pilots in Spain - says it is going to sue the airline after a year of failed talks. But it has also threatened to move part of its fleet to Poland, which could mean a loss of jobs.
Last night, Ryanair said "it took every step to minimise disruption" to passengers.
Since the it first recognised unions in December 2017, walkouts have been staged multiple times by Ryanair staff in various countries.
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"We want to again apologise to customers affected by this unnecessary disruption and we ask the striking unions to continue negotiations instead of calling anymore unjustified strikes".