Thomas Cook's decision was part of an audit of 49 animal attractions.
Holiday agency Thomas Cook will stop visits to all animal attractions that have orcas in captivity as part of its ongoing animal welfare policy.
Nearly 18 months ago Thomas Cook announced an independent audit of 49 animal attractions it sold tickets too.
Thomas Cook has since "removed" 29 of them for not meeting the Association of British Travel Agents standards required.
On Sunday, Chief Executive Peter Frankhauser said despite two attractions passing the audit, Thomas Cook would no longer sell any animal attractions that keep orcas in captivity.
The two attractions referred too are SeaWorld in Florida and Loro Parque in Tenerife (Spain), according to the BBC.
"Today we are announcing a new addition to our animal welfare policy based on that same principle. From next summer, we will no longer sell any animal attractions that keep orcas in captivity," he wrote in a blog post.
"Today’s announcement will see Thomas Cook remove two attractions which we currently offer customers, both of which passed our audit process and made improvements to the way they treat animals," he added.
The decision comes as 90 percent of customers made it clear to the company they found it important their holiday company takes animal welfare seriously.
SeaWorld Parks & Entertainment said in a statement that it had stopped breeding orcas and the animals in its care will remain for "many years to come".
“Millions of UK guests have visited our parks for fun and learning. They have seen firsthand the incredible care we provide all of our animals and learned about how we are protecting and saving species in the wild," the statement to SBS News read.
"We have ended breeding for orcas, however, the current animals in our care will be with us and our visitors for many years to come. We will continue to welcome the public into our parks for the unmatched experiences we create every day.”
The captivity of orcas has been under the spotlight in recent years following the release of the controversial 2013 documentary Blackfish.
The documentary tells in detail how Tilikum, a killer whale, killed 40-year-old animal trainer Dawn Brancheau at SeaWorld theme park in Orlando, Florida.