About 150 workers from Coke's Northmead factory, in western Sydney, voted to take industrial action which the union said could put the popular drink in short supply for Christmas.
The move comes days after Woolworths' distribution centre workers secured a pay rise following a 17-day strike.
Electrical Trades Union NSW secretary Allen Hicks said Coca-Cola treated staff with contempt and workers would be far better off at Pepsi.
Coca-Cola factory workers are paid less than their counterparts at Pepsi, a union official says. (James Ross/AAP PHOTOS)
"Despite doing the same work, workers in Coca-Cola's Northmead factory are paid significantly lower than those working for Pepsi," he said.
"Coca-Cola has a two-tiered wage system which sees some employees paid significantly less than their co-workers, even though they're doing exactly the same job."
Coke workers also have issues with rostering and the company's progression structure.
Mr Hicks said it was a new take on the age-old "Coke vs Pepsi" debate.
"All these workers want is to be paid in line with industry standards … when it comes to treating its employees with respect, Pepsi is winning hands down," he said.
Woolworths reached a deal on Friday to reopen its distribution centres and end a 17-day strike.
After months of negotiations, the United Workers Union said it had secured wage increases above the rate of inflation and a new clause would be added to workplace agreements "that ensures that the workers will not be disciplined for the speed that they can work at".
Woolworths said its four warehouses would be back to full capacity as soon as possible.
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