The Dublin-based airline said the loss, which compared with an €18m profit last year, was in line with guidance, and left its full-year profit forecast unchanged at €510m.
Chief executive Michael O'Leary said the carrier had responded to weaker conditions in September with lower fares, seat promotions and increasing its advertising and marketing spend.
Those moves stimulated traffic, which grew by 6% to 18m passengers over the quarter. It also pushed forward bookings for quarter four ahead of last year's, although the firm said yields are lower.
Third quarter revenue per passenger fell by 6%, with a 13% rise in sales of ancillary items, such as reserved seating, priority boarding and higher credit card fees, offset by a 9% fall in fares. Shares closed up 0.43p at 6.74p