The airline and operator will end Manchester-Jersey services on 28 June, while its twice-weekly Stansted-Jersey and Birmingham-Jersey services will go down to weekly.
It will continue to operate its Leeds Bradford-Jersey route three times a week, Newcastle-Jersey once a week and East Midlands-Jersey once a week.
A Jet2.com and Jet2holidays spokesperson stressed the decision was unrelated to the widely reported staff shortages currently affecting the aviation sector.