Expedia’s booking platform will also provide all city break and hotel-only sales across Cook’s distribution channels in Europe.
Cook said the multi-year agreement would provide its customers with more than 60,000 extra hotels in global city and European domestic locations than currently on offer.
It said the deal would also enable it to "significantly reduce the cost and complexity" of its city breaks and hotel-only business.
Expedia’s technology will deliver bookings for city and domestic hotels, either on their own or as part of a city break dynamic package, through Cook’s primary websites, contact centres, stores and distribution to affiliated travel agents.
Additionally, the agreement gives Cook the option to offer its sun and beach package holidays on Expedia sites globally, broadening its distribution reach.
Thomas Cook chief executive, Peter Fankhauser, said: “The combination of Expedia’s portfolio of hotels and best-in-class online technology will transform Thomas Cook’s city breaks and hotel-only offer for customers while helping the business take an important step forward in delivering our strategy for profitable growth.
"Joining forces with a company that has the global reach and expertise of Expedia will allow Thomas Cook to further simplify our systems and processes.
"At the same time, this will free us up to focus on holidays to our own-brand and selected partner hotels in sun and beach locations where we know we can really make a difference to customers. I am confident this marks the first step in a long-term and mutually beneficial relationship with Expedia.”
Expedia brand president, Aman Bhutani, added: “We’ve always had profound respect for the Thomas Cook brand and we believe that our coming together will enhance our abilities to help more people to get out and see the world, while enhancing each of our competitive positions in the European market."
Cook said the deal with Expedia was a "major step forward" in Thomas Cook’s group-wide transformation programme, and follows the announcement in August 2016 of a hotel sourcing deal with Webjet, covering the bulk of Thomas Cook’s complementary sun and beach hotel offering.
Cook added that the agreement with Expedia would also help to "reduce the complexity of Thomas Cook’s business, acting as a catalyst to significantly simplify and streamline operations" across its 16 source markets.