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. Prior to that, she directed the company's global strategy and was the primary architect of PepsiCo's restructuring.
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 role of continuing as PepsiCo's CEO requires."
Nooyi's current responsibilities will be divided between Richard Goodman, chief financial officer of PepsiCo International, and Hugh Johnston, senior vice president of transformation, who is promoted to the role of executive vice president of operations.