The World Society for the Protection of Animals (WSPA) will auction "rights" to a whale's life on the online site.
WSPA wants to raise $180,000 (£95,000), the value of meat from a fin whale; it then aims to pay this sum to hunters, and ask them to let one whale go.
Iceland's return to commercial whaling after a 20-year halt has brought diplomatic protest from many quarters.
On Wednesday, a group of 25 countries delivered a demarche, a formal letter of protest, to the Icelandic government through their ambassadors in Reykjavik.
Parts of a whale
The eBay auction is WSPA's attempt to involve the public, in Britain and elsewhere.
People logging in to the site will be able to pledge sums of £10 or more, in the hope of building up to the price of a fin whale's meat.
"We're asking the public to go and bid for the life of this whale, and send Iceland a message that the public will not stand for the hunting of these whales," said WSPA's campaigns director Leah Garces.
WSPA acknowledges that Icelandic whalers or the Reykjavik government may refuse to accept money raised this way, even assuming the public pledges enough.
But Ms Garces denied the idea is a gimmick, telling BBC News: "The idea is to raise in Iceland's mind that this is not acceptable."
If Iceland will not take the money, WSPA says it will put sums raised towards its whaling campaigns.
Iceland announced last month that it would resume commercial whaling after a break of 20 years.
It intends to hunt 30 minke whales and nine fins over the coming year. The fin whale is categorised as endangered on the internationally-recognised Red List of Threatened Species.
The Icelandic government has reacted calmly to the demarche, saying that protests made against other whaling nations such as Japan and Norway had not resulted in any breakdown of diplomatic relations.