Coca-Cola's brand and logo has become part of US culture
According to the claims, administration worker Joya Williams went through files and stuffed a new Coca-Cola product and documents into her personal bag.
Also accused of stealing trade secrets are Ibrahim Dimson and Edmund Duhaney.
PepsiCo said it co-operated with the FBI and Coca-Cola after being contacted by someone looking to sell information.
Coca-Cola said the secret formula of its main drink - sold in the distinctive red and white cans - had not been compromised.
Its chief executive, Neville Isdell, wrote in a memo to staff: "Information is the lifeblood of the company".
Coca-Cola, he wrote, would be reviewing its security procedures.
Dave DeCecco, a PepsiCo spokesman, said that the company was happy to have helped out its rival.
"Competition can sometimes be fierce, but also must be fair and legal," he said.
'Valuable secrets'
According to investigators a letter was sent to PepsiCo in May from someone calling themselves "Dirk" and claiming to be a high-level employee at Coca-Cola with information to trade.
An undercover FBI agent claims to have met with Mr Dimson, who was said to be posing as "Dirk", at Hartsfield-Jackson International Airport in Atlanta in June.
During that meeting, Mr Dimson is alleged to have handed over an envelope containing documents and a glass bottle containing a liquid sample.
Coca-Cola's recipe has been made a trade secret for 120 years
The undercover officer claims to have paid "Dirk" $30,000 (£16,000) and promised to pay another $45,000 at a later date.
On 27 June, another agent offered to buy the remaining trade secrets for $1.5m, and it is alleged that two of the suspects opened a bank account in order to receive the funds.
The three suspects were arrested on 27 June.
Investigators say they have footage showing Ms Williams going through files and "holding a liquid container with a white label, which resembled the description of a new Coca-Cola product sample, before placing it into her personal bag".
Ms Williams, Mr Dimson and Mr Duhaney are due to appear before magistrates in Atlanta, Georgia on Thursday.
"We are committed to protecting the intellectual property that is so critical for our corporate citizens to remain successful in the 21st century economy," said US Attorney David Nahmias said.
"Theft of valuable trade secrets will not be tolerated, not by the Justice Department and not even by competitors, as this case shows," he added.
Three people have been charged in the United States for trying to sell Coca-Cola trade secrets to PepsiCo. The main suspect, administration worker Joya Williams, tried to sell documents and a liquid sample of a new Coca-Cola product to the rival, prosecutors said.

When being offered to buy the trade secrets in May, PepsiCo immediately contacted the FBI. A person calling himself "Dirk" wanted to meet a PepsiCo representative at Hartsfield-Jackson International Airport in Atlanta in June. Instead, an undercover FBI agent met with Ibrahim Dimson, the man posing as "Dirk".

During the meeting it is said the undercover agent gave Dimson $30,000 for the trade secrets and promised to pay an additional $45,000 later. Then later that month, another agent later offered to buy the remaining trade secrets for $1.5m. The same day the suspects were arrested.

A third person, Edmund Duhaney, was also arrested.

PepsiCo said in a statement that "competition can sometimes be fierce, but also must be fair and legal".

Coca-Cola said that it would review its security measures. The corporation's top-secret formula of its main drink was not affected in this security breach.