She will succeed Richard Taylor in February, who is leaving Macmillan to pursue a career in executive coaching.
Rowney joins from Save the Children UK, where she has been the executive director of fundraising and marketing since early 2017.
Prior to this, Rowney spent 13 years at Cancer Research UK, leading its Race for Life and Stand Up To Cancer programmes, as well as working in innovation and corporate partnerships.
"Claire brings a huge breadth of experience from across the charity sector," Macmillan Cancer Support chief executive Lynda Thomas said.
"This, combined with her energy and passion for the work we do, will be invaluable in ensuring we continue supporting the growing number of people living with cancer to live life as fully as they can."
Rowney said she was "thrilled" to be joining Macmillan’s fundraising, marketing and communications team.
"The services it offers are absolutely vital, and with the number of people with cancer rapidly growing, raising funds to deliver this support has never been more important," she said.
"I am looking forward to building on Macmillan’s successes to ensure we can be there for even more people living with cancer."
Macmillan was recently ranked the fourth most valuable UK charity with a brand valuation of £910m in a Morar HPI league table.