There are a total of 180 people employed across the 39 stores - Cook’s total retail staff in the UK is 5,500.
The move comes after the operator closed 28 high street stores between October and December last year.
A Thomas Cook spokesperson confirmed that the split of Co-operative Travel stores closing versus Thomas Cook shops shutting was “about half and half”.
In December it was announced that Thomas Cook would take full ownership of its UK retail network after the Co-operative Group exercised its “put option” on a joint venture between the firms.
At the time of the announcement, there were 556 Thomas Cook stores and 208 Co-operative Travel branches, totaling 764. Now, there are a total of 757 stores in the network.
Today, Thomas Cook said the 39 upcoming nationwide closures would be in areas already well-served by other Thomas Cook shops, to “ensure it is focused in locations where customers want to visit”.
When complete, Thomas Cook will have 719 stores.
The operator said the affected stores were either in areas where there were too many stores in close proximity, or had seen a decline in footfall which had impacted profitability.
Discussions have begun with the employees affected with the hope that “the majority can be redeployed across the business to retain their expertise”.
The spokesperson said the consultation period would last “a number of weeks”.
According to the government’s website, there’s no time limit on how long redundancy consultations last, but there is a minimum period before an employee can be dismissed.
For 20-99 proposed redundancies the minimum consultation period before dismissal is 30 days, and for 100 or more proposed redundancies the period is 45.
Thomas Cook has also announced its first step in consolidating its store network into one high-street brand by refurbishing and rebranding 57 Co-operative Travel shops.
The aim is to move all stores to the Thomas Cook brand by November 2018.
As part of “network improvements”, Thomas Cook will open a new Discovery store this spring in Silverburn, Glasgow.
With three openings last year – in Westfield Stratford City, Chelmsford and Belfast – Discovery stores are focused on higher footfall areas such as shopping centres “and have already proven very popular with customers thanks to the fresh new design, dedicated kids areas and interactive video content”.
As well as new stores, Cook is planning a rolling programme of refurbishments of existing stores in high footfall areas to the new format, with the aim of having 25 Discovery stores by the end of 2019.
Kathryn Darbandi, director of retail and customer experience for Thomas Cook UK & Ireland, said: “We’re continually reviewing our network of stores across the UK to ensure that they’re doing the best job they can in engaging customers in the great range of holidays Thomas Cook offers.
“While we’ve seen strong growth in our online sales, we also know that more than two thirds of customers who
research online come into store, valuing that face-to-face contact with our travel experts.
“The changes we’re making ensure that we’ve not only got the right stores where customers most need them but also that we’re creating an experience that they will recommend to their family and friends.”
Cook would not reveal the location of any possible closures.