The nine routes from Manchester that will close are those to Barcelona (Girona), Bremen, Brussels (Charleroi), Cagliari, Dusseldorf (Weeze), Frankfurt (Hahn), Marseille, Milan (Bergamo) and Shannon.
The changes, affecting 44 flights a week, will take effect from 1 October.
The airline said passengers affected by the changes would be e-mailed and, "provided with a full refund, or the alternative of flying to some destinations" from East Midlands, Leeds Bradford and Liverpool.
Ryanair said it had offered Manchester an additional 28 weekly flights if the airport agreed to reduce its charges, but that it had rejected the offer.
However, a spokesman for Manchester Airport said it did not "believe that charges as low as £3 per passenger are unreasonable".
"We've consistently cut our charges for the last 15 years even when faced with increased costs such as security," he added.
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