The 56-year-old’s appointment is effective July 15, 2020.
Mr Agbaje will join the Board and the Audit Committee.
Until his appointment, Mr Agbaje was the Managing Director and Chief Executive Officer of Guaranty Trust Bank plc, a Nigerian multinational financial institution.
Agbaje also currently serves as a director of MasterCard Advisory Board Middle East and Africa.
He holds a Bachelor of Science in Accounting and a Masters in Business Administration from the University of San Francisco.
The Chairman and CEO of PepsiCo, Ramon Laguarta said "I am delighted to welcome Segun to the PepsiCo Board."
"Segun is a well-respected and proven business leader with a deep understanding of complex businesses and fast-growing markets, particularly Sub-Saharan Africa where we recently acquired Pioneer Foods as part of our strategy to expand in the region. His experience in business transformation and passion for delivering consumer value will serve PepsiCo well as we continue our journey to be the global leader in convenient foods and beverages by winning with purpose," he added.
Mr Agbaje was appointed as MD of Guaranty Trust Bank plc in 2011. He joined the bank 1991 and held several positions there, including Executive Director and most recently Deputy Managing Director from 2002 to 2011.
Mr Agbaje had earlier worked as an auditor for Ernst & Young LLP in the United States from 1988 to 1990.
The chair of the Board's Nominating and Corporate Governance Committee Daniel Vasella said "We look forward to Segun joining the PepsiCo Board and to the valued global perspective he will add to our team. His knowledge and experience of embracing and scaling new technologies and critical capabilities will be valuable as we continue to invest in opportunities that create shareholder value and deliver long-term sustainable growth."