Nooyi, who has worked at PepsiCo since 1994, takes up her new role on 1 October, replacing Steve Reinemund.
She moves up from the role of president and chief financial officer, a position she has held since 2001.
Reinemund has been chairman and CEO of PepsiCo since 2001. He retires in May next year.
He said: “After 22 years with PepsiCo, more than five of them as chairman and CEO, I have decided that my family is entitled to more time from me than the responsibilities and obligations of continuing as PepsiCo's CEO requires and deserves.”
Reinemund added: “Indra's record of transforming PepsiCo speaks for itself, and she has been an invaluable partner and ally throughout my time as CEO. I am convinced she is more than qualified and clearly ready for her new role leading PepsiCo.”