Syed is leaving to “pursue external opportunities”, the company said, with Mottershead taking over on October 1.
Syed will stay with the business until October 31.
In a statement released today, Thomas Cook chief executive Peter Fankhauser said: “Next year marks the 175th anniversary of our company, and Chris is the ideal person to lead the UK business into the next chapter in its history.
"He enjoys an excellent reputation, with a well-proven vision of meeting the needs of customers in an omni-channel, technology-driven world.
"His considerable experience within the industry will contribute significantly to the team’s effectiveness and focus, and I am confident that the UK business performance will go from strength to strength under his stewardship.”
Mottershead added: “I am delighted to have been entrusted with helping to build and shape the future of the UK business at such an important time in its history.
“The company has a great heritage and I feel proud and privileged to have been given the opportunity to help further establish Thomas Cook as the preferred choice for the UK travel consumer.”
Syed has been in the position for just over a year. He joined the company in 2013 as managing director of Cook’s Western and Eastern European business.
He was one of a number of ex-Premier Farnell staff who moved over to Cook alongside former boss Harriet Green. Many of these recruits have since followed Green out of the business, including the the likes of Rob Rospedzihowski, Marco Ryan, and Sandra Campopiano.
Mottershead left Tui to join Cook in March, originally as business development director, before he was promoted to commercial director in July.
He started his travel career with Airtours in the early 1990s before joining Tui as UK managing director. He also founded the now-defunct Travelzest.