Wizz Air flew just 1.56m passengers last month, down 20% from August.
As quarantine rules are impacting airlines, Wizz Air reported a 60% drop in passengers compared the September previously.
The airline flew almost four million passengers in September 2019, compared to 1.56 million in September 2020.
Despite the new quarantine rules still in effect, the airline said it is continuing to expand across Europe.
Other airlines are also feeling the effects of the pandemic and limited travel.
Ryanair flew 5.1 million passengers in September, compared to the 14.1 million the same period a year ago.
A spokesperson for the airline said: “However, as customer confidence is damaged by government mismanagement of Covid travel policies, many Ryanair customers are unable to travel for business or urgent family reasons without being subjected to defective 14-day quarantines.”
Airlines have called on the government to make a change to the current quarantine rules and introduce airport testing.