"The Coca-Cola sign has been an iconic part of the Kings Cross skyline for more than 40 years," said Coca-Cola South Pacific president Roberto Mercadé.
"It's one of Sydney's most internationally recognisable landmarks and we knew we had to find a way to keep a part of the old sign alive. What better way than to help a great local charity like the Wayside Chapel in the process?
"We will not only find new homes for the old sign but also have the opportunity give back to the Kings Cross community by raising money for people who need it most."
The results of the eBay auction will be announced at the official switch-on of the new sign in mid-September.
Coke will start the bidding at AU$100 (NZ$104) apiece but hasn't said how much it hopes to bring in.
Wayside Chapel Pastor Graham Long said it was a surprise when Coke approached the charity, but "naturally anyone who wants to donate money is fine with me".
"Kings Cross is a place people come for a good time, but also a place where people come and overdo it and burn out, and in that case we're here," he said.
"Any money they give us will go towards helping those people. Most are people who are homeless, rough sleepers or in dodgy boarding houses. Those issues go hand with mental illness, drug addiction and health issues."
Pastor Long said the Chapel, which runs on 90 per cent donations and 10 per cent government funding, would use the money to fund its cafe and other essentials like clean underwear and clothes.
We will not only find new homes for the old sign but also have the opportunity give back to the Kings Cross community by raising money for people who need it most.
"People who come off the street usually need a new pair of undies," he said. "Nothing says 'I love you' like a clean pair of undies."
It won't be the first time an iconic piece of a city's skyline was sold on eBay. In 2005, the original Hollywood sign, which was torn down in 1978 and thought to be lost, was sold for $US450,000 by entrepreneur Dan Bliss.
A spokeswoman for Coke said while the reserve for each letter starts at $100, "it's impossible to measure the true value of these 1974 original, one-of-a-kind pieces".
"However, there is a strong precedent for iconic signs and symbols being sold on eBay - last year the Sydney Olympic Rings sold for $26,000. We do hope that people recognise how special these are so we can raise as much money as possible for our friends at The Wayside Chapel."
The auction itself is co-ordinated by eBay's charity partner, Bid For Good, who manage and co-ordinate the entire auction process.
Coca-Cola South Pacific together with Bid for Good will work with the winning bidder to co-ordinate the logistics from the Girraween warehouse in Sydney, to "almost anywhere in the world".