The tour operator said the decision was made because of customer feedback and evidence from animal welfare specialists.
The announcement was made by the company's boss Peter Fankhauser in a blog posted on Sunday.
"This was not a decision we took lightly," he wrote.
"We have actively engaged with a range of animal welfare specialists in the last 18 months, and taken account of the scientific evidence they have provided.
"We have also taken feedback from our customers, more than 90% of whom told us that it was important that their holiday company takes animal welfare seriously.
"That has led us to the decision we have taken today."
From next summer, the travel agent will no longer offer tickets to any attractions where captive orcas are kept.
The decision will see Thomas Cook stop selling trips to two attractions - SeaWorld and Loro Parque, in Tenerife.
Both had passed the firm's audit process, which saw 29 other attractions removed from its books, following the announcement of a new animal welfare policy around 18 months ago.
Mr Frankauser said: "We respect and applaud the work that has been done, and we will work with both over the next 12 months to prepare for our exit.
"We will also continue to work ourselves to identify more sustainable alternatives."
The move follows a public backlash towards keeping killer whales in captivity that gathered pace after the release of the 2013 documentary Blackfish.
The film argued that orcas held in captivity become more aggressive towards humans and each other.