Waugh joined the luxury brand in January 2014, after ten years at Starbucks, where she was head of marketing, marketing director and EMEA director of strategic programmes.
She will start at Jack Wills next month and report to chief executive and founder Peter Williams.
Williams said: "I absolutely believe that Claire has the vision, talent and drive to help market the brand around the globe effectively to our many different customers and in a way which fits the very unique brand DNA of Jack Wills.
"Coming from Burberry, Claire has a fantastic understanding of fashion and beauty all of which will be directly relevant to her work at Jack Wills."
Williams said that a number of other new people were set to join the senior management of the business before the end of the year.