The Irish airline has attracted heavy criticism for the cancelled flights and a perceived lack of urgency in offering compensation.
Last week, it announced a further 18,000 flights for the winter season had also been cancelled.
The airline added that it had refunded/re-accommodated 98% of customers who were affected in September and October, while it was still waiting to hear from the final 2%.
Some 11.8 mln passengers were carried in the month to September 17 against 10.8 mln the previous year, in spite of the cancellations, which it blamed on a change in the holiday year to January to December from April to March.
Load factor, or how full the planes were, rose by 2 percentage points to 97%.
Rival WizzAir PLC (LON:WIZZ), meanwhile, reported another surge in traffic over the same period. Passenger numbers rose by 26% in September to 2.7 mln with the load factor rising by 1.3 percentage points to 92.9%.
The airline did not say if it had received a boost from disgruntled Ryanair passengers switching carriers.
'Passenger numbers no guide to profitability'
Neil Wilson, senior market analyst at ETX Capital said: "Of course it is too early to assess reputational damage from these figures, but it does signal that it is still enjoying strong growth fuelled by price cuts. And demand in the European short-haul budget sector appears robust as Wizz Air has also reported a big jump in passengers.
“But as the recent airline failures show, passenger numbers alone are not a particularly good indicator of health. Monarch carried 14% more passengers last year but for £100mlm less revenue. Airlines continue to cut fares to grow market share and this is coming at the expense of profit margins. The problem of over-capacity and overly-aggressive pricing is not going away until we see more consolidation.”
Ryanair shares were flat at €16.90, while WizzAir added 0.5% to 3,014p.
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