Chief executive Michael O'Leary described the third-quarter loss of €19.6m (£17.1m) as "disappointing", but said it was entirely due to a 6% decline in air fares.
Ryanair maintained its full-year profit guidance of between 1 billion euros to 1.1 billion euros.
Stronger ancillary revenue growth, of 26 per cent to €557 million for the quarter, was again offset by higher fuel, staff and Brexit preparation costs.
Over the same period previous year it made a €106m profit after tax.
In December, Ryanair acquired the remaining 25 per cent of Laudamotion. Plus a share price down 40 per cent in 18 months.
The company said it can not rule out further cuts to air fares and slightly lower full-year guidance as a result of Brexit.
Mr O'Leary said: "The risk of a no-deal Brexit remains worryingly high".
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The airline said it flew 32.7 million customers in the quarter, an increase of 8%, and recorded revenue of €1.53 billion - up almost 10%. O'Leary has signed a new five-year contract that will keep him in the role until at least July 2024. "While we hope that common sense will prevail, and lead to either a delay in Brexit, or agreement on the 21-month transition deal now on the table, we have taken all necessary steps to protect Ryanair's business in a no-deal environment", the company said.
And even if the shareholders might claim they saw off the airline's "legend" of a chairman David Bonderman and its senior independent director Kyran McLaughlin, neither is going until September 2020 - after 24 and 18 years, respectively.
"In our view, Ryanair remains the long-term victor in the European airline industry, based on its leading market position, extensive network, low unit costs and strong balance sheet", said analysts at stockbroker Liberum in a note to investors.
In order to ensure a smooth succession, Stan McCarthy, who joined the board in May 2017, has agreed to take up the position of deputy chairman from April 2019, and will transition to chairman of the board in summer 2020.
CEO O'Leary will become CEO of a larger Ryanair Group, which will include four subsidiaries: Ryanair DAC (the main airline, ) Laudamotion, Ryanair Sun and Ryanair UK.
Ryanair has announced plans to move to a group structure similar to that of International Airlines Group over the next 12 months.
Ryanair has come under pressure recently to shake-up its leadership, with 30 per cent of shareholdings voting against Bonderman's re-appointment as chair at the company's annual meeting in September.