"We have managed to maintain our traffic to and from our three Barcelona airports but only by reducing our prices by about 30 percent," Michael O'Leary, head of the low-cost carrier, told reporters in Madrid.
"If traffic numbers are holding up, it's only because traffic airfares have fallen by 30 percent.
"That is a real challenge for us going forward."
Ryanair flies to the cities of Barcelona, Girona and Reus in Catalonia.
O'Leary said the decision to reduce prices was taken in October just as the world's cameras focused on mass protests in Barcelona after a banned independence referendum was marred by police violence.
"There's a nervousness in passengers booking to Catalonia, particularly travellers on city breaks, in the UK, Ireland, Germany," said O'Leary.
The uncertainty caused by the ongoing independence crisis has impacted the tourism sector in the much-visited region which has seen a 10 to 15 percent drop in turnover.
More than 3,200 companies have also moved their legal headquarters out of Catalonia.
According to a report by the BBVA bank, Catalonia will this year create "35,000 fewer work positions compared to what would have been created without uncertainty."
But it adds the "outlook for the first quarter of 2018 is still good."