Clifton will take up the appointment in April following the completion of Jeremy Bullmore's five-year term.
Clifton joined brand consultancy Interbrand in 1997 as chief executive in London before becoming chairman in 2002.
She started her career at DMB&B and then moved to J Walter Thompson.
In 1986 Clifton joined Saatchi & Saatchi, progressing in 1992 to director of strategic planning and in 1995 to executive planning director and vice-chairman.
During her time with the agency she worked with clients including Procter & Gamble, British Airways, Visa International, PowerGen and British Telecom.
Clifton has also been involved in several government projects on environmental and communication issues. She served on the Sustainable Development Commission with Sir Jonathon Porritt for five years and is a trustee of wildlife conservation charity WWF.
David Barr, MRS director general, said: "Over many years, MRS has benefited enormously from the contribution to strategic direction made by distinguished presidents.
"We have been extremely fortunate in many key debates of the last five years to have had access to the knowledge, wisdom, and humour of Jeremy Bullmore.
"Now we look forward to having Rita Clifton as our president during the next important phase of our development."
Clifton said: "I have great respect for the work of the MRS.
"I very much look forward to getting formally involved, although stepping into Jeremy's rather large shoes will be a test.
"It does seem to me that there are some big challenges and opportunities for the research world over the next few years and it will be exciting to be able to contribute what I can."