Ryanair's website declined on Monday for several hours – but the airline was still charging £ 55 if it arrived at the airport.
The website of the budget operator and the mobile application collapsed, leaving customers unable to check in.
The Ryanair site is also offline on Tuesday morning and a exploitation page said it is "currently out of service for maintenance."
Frustrated customers complained about social media after the airline's refusal to waive the late check-in charge.
The YouTube Technology Reviewer and blogger @TotallydubbedHD said he was given an additional £ 110 account for late check-in on two return flights of £ 46. He said Ryanair's customer service declined to recognize that the site had fall down.
Twitter's @HeatherMatthews complained that he was also hit by a £ 55 fine in Liverpool to be unable to check online.
He added: "I tried to use the online complaint form and this also shows an error message. What do I do? @Ryanair."
Another customer stated that he was accidentally paid for the same flight twice due to a malfunction of the screen and did not receive a confirmation of the two bookings.
At 21:00 on Monday night, the budget airline told the Press Association that its website was functioning properly and that "a short server issue" was quickly resolved. However, the site was still offline at 10.20pm.
Never I contacted Ryanair, an airline spokesman declined to acknowledge that the site had fallen on Tuesday or to confirm whether a passenger flight would now charge a £ 55 charge if it did not check in.
Earlier this month, the airline received its website and mobile offline for 12 hours for urgent upgrade, but was still charging passengers if they were unable to check in on the internet.
Additional reports from PA