The company, which is based in Leeds, will not operate any flights to Krakow until May 27, when there will be a “phased restart”.
It usually runs two flights a week to the Polish city, from Leeds Bradford Airport, Newcastle, Manchester, Birmingham and Glasgow.
A Jet2 spokeswoman said: “Due to current circumstances, we have taken the decision to suspend our flights and city breaks programmes to Krakow from March 24, up to and including May 26.
“Where customers are affected by any programme changes, we will automatically cancel their booking with a full refund.
“We are planning a phased restart to Krakow from May 27 and we will of course keep customers updated.”