Ryanair managed to push carryings up by 10% to 11.8 million last month despite its pilot holiday rota “mess up”.
The budget carrier’s load factor rose by two percentage points year-on-year to 97%.
The September result gave a 12% rise in the rolling annual total of passengers carried to 127.3 million.
Chief marketing officer Kenny Jacobs said: “These figures include the 2,100 flight cancellations announced for September and October.
“We have now refunded/re-accommodated 98% of customers who were impacted in September and October. The remaining 2% of affected customers have yet to contact us.
“We again sincerely apologise to our customers for these deeply regretted cancellations.”
Rival low cost carrier Wizz Air saw a 26% jump in passenger carryings last month.
The eastern and central European airline flew 2.1 million passengers in September as its network continued to expand.
The load factor grew by 1.3 percentage points over the same month last year to 91.6%.
The airline took delivery of a new Airbus A321ceo, taking the fleet number to 86 aircraft.
Wizz Air also introduced a new ancillary offering giving further flexibility to customers who can now book up to 10 tickets and name their travel partners later at the time of check-in.