The cancellations come after hundreds of passengers were stranded at London’s Stansted Airport as a result of storms on Tuesday.
The latest disruption is a result of industrial action by pilots in Ireland, Germany, Sweden, Belgium and the Netherlands.
Staff are holding a 24-hour walkout over pay and conditions.
A total of around 400 flights Europewide have been cancelled due to the strike action, AFP reported – equating to around 55,000 passengers.
A check on the Ryanair website by Sky News early Friday morning found at least 50 flights listed as cancelled between destinations in the affected countries and the UK.
When Sky News requested a list of all the flights cancelled today, Ryanair said they would not supply that information.
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.
The Ireland-based budget airline said the industrial action was “regrettable and unjustified” and called for unions to return to the negotiating table.
Customers have been notified and a majority of those affected moved to another Ryanair flight, the company said.
A spokesman said that despite the walkouts, 85% of Ryanair’s scheduled flights, more than 2,000, would operate as normal.
He said: “Ryanair took every step to minimise the disruption and we notified our customers as early as possible advising them of their free move, refund or reroute options,” the carrier said.
“The majority of customers have already been accommodated on another Ryanair flight.
“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.”
Germany’s powerful Cockpit union accused Ryanair of “categorically” ruling out higher personnel costs for cockpit crew, leaving no room for a compromise.
“Ryanair alone is responsible for the escalation we are now seeing,” Cockpit president Martin Locher told a news conference on Wednesday.
A judge later ruled that Dutch pilots could join the strike.
The airline was also hit by disruption earlier in the summer, when 100,000 travellers to and from Belgium, Ireland, Italy, Portugal and Spain, were affected.
Ryanair also narrowly avoided strikes at Christmas last year by agreeing to recognise unions.
Ryanair’s chief marketing officer Kenny Jacobs said the company’s German pilots earn up to €190,000 (£171,000) a year.