While Nooyi steps down the day she completes 24 years with the company, she will remain as the chairman until early 2019.
Nooyi will be succeeded on October 3 by Ramon Laguarta, who has served as Pepsi's president since previous year.
CEO of PepsiCo Indra Nooyi speaks at the Bloomberg Global Business Forum in New York City, US, September 20, 2017. "Laguarta was also elected to the company's Board of Directors, effective October 3rd", the statement also said. She will remain as chairman until early 2019.
Laguarta, Nooyi successor, has held a number of executive and general management roles in his 22 years at PepsiCo.
"Leading PepsiCo has truly been the honour of my lifetime, and I'm incredibly proud of all we have done over the past 12 years to advance the interests not only of shareholders, but all our stakeholders in the communities we serve", Indra said.
Nooyi took to micro-blogging site Twitter to express her "mixed emotions". "PepsiCo's best days are still ahead of it". "This company has been my life for almost a quarter century and part of my heart will always remain here", Nooyi said in a prepared statement.
She will be replaced by Ramon Laguarta, who will become the beverage maker's sixth CEO. "She has delivered strong and consistent financial performance, managing with an eye toward not only the short-run, but the long-run as well".
She said the shift toward healthier products required totally realigning the company's "innovation, marketing, execution and budgets" - and then changing the company's culture.
Nooyi was named as Fortune's second most powerful woman in business past year, coming after chairman and CEO of General Motors, Mary Barra. Dividends per share almost tripled from $1.16 in 2006 to $3.17 in 2017 and a compound annual growth rate of almost 10%, according to a PepsiCo statement. He had previously been CEO of the European and sub-Saharan African unit of Pepsi before being named the company's president.