The firm’s boss called for “openness and transparency” on coronavirus data so that the industry and its customers could better understand the decisions behind the government's three-weekly review.
It comes after several changes to the travel lists – including moving Portugal from “green” to “amber” – were announced by the transport secretary.
Jet2 said in a statement: “Following today’s update, we have taken the decision to restart flights and holidays on July 1 2021.
“For any destinations currently on the Amber List, we are also allowing customers to amend their booking free of charge if they are due to travel between July 1 and July 21 2021.”
Steve Heapy, CEO of Jet2.com and Jet2holidays said: “We know how disappointed our customers and independent travel agency partners will be following today’s announcement, and we share their concerns and frustrations.
“We are now calling for complete openness and transparency when it comes to the data, so that customers and the industry can really understand what is driving these decisions.”
“We agree that public health must be the number one priority. However, despite all the evidence and data showing that travel can restart safely and at scale, the UK continues to remain largely grounded whilst the rest of Europe opens up.”
Listen to the ITV News coronavirus podcast
Jet2 said flights to Turkey, which remains on the “red” list, would not restart until July 22.
It added that customers affected by changes to the programme would have their bookings automatically cancelled and would be given a full refund.
The changes to the travel lists mean anyone travelling back from Portugal to the UK - from 4am on Tuesday June 8 - will have to spend 10 days in quarantine and ensure they can pay for two PCR tests.
Why were no countries added to the green list? Digital Video Producer Natalia Jorquera explains
It is likely to spark frustration amongst those who have booked trips to the country - including those who travelled to Porto for the Champions League final as well as Brits travelling to popular tourist destinations such as the Algarve.
Stay up to date with the changing travel situation in the UK and abroad with news, information and advice at itv.com/holidaynews