"Due to increased costs we don't have any financial alternative but to close our Bordeaux base in November," the company's commercial director Jason McGuinness said in a statement released in French.
The airline has been operating around 40 flights to and from Bordeaux.
In the statement it said the three planes and 90 staff currently based at the Bordeaux airport would be transferred to other, less costly, bases within its network.
READ ALSO Are France's loss-making regional airports under threat?
Ryanair CEO Michael O'Leary said in March that Bordeaux airport was seeking to double its fees and warned he would shut the base rather than pay that amount.
Bordeaux-Merignac airport said it had "put limits on the financial demands" of Ryanair and would pursue its strategic objective of diversifying the airlines which use airport.
"We don't wish to see a company which has been installed in Bordeaux for 14 years leave," the airport told AFP.
"If it would like to work again in Bordeaux, it will be welcome," it added.
Bordeaux-Merignac in 2023 was the eighth busiest French airport with 6.6 million passengers.
However, this figure is just 85.5 percent of pre-Covid 2019 levels whereas the average for French airports was 92.7 percent.
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