BHP said in December it would quit the group but gave it a few months to respond.
Now the miner has confirmed its exit.
"In light of the material difference identified by the review and the narrow range of activities of benefit to BHP from membership, BHP has reached a final view that it will cease membership of the WCA," it said in a statement.
Advocacy group the Australasian Centre for Corporate Responsibility pointed BHP towards the move but said there was more to do still after the WCA confirmation because the miner had stayed part of the Minerals Council of Australia and the US Chamber of Commerce.
"This is the time for decisive action, and BHP has baulked," ACCR executive director Brian Flynn told the Australian Financial Review.
"The [BHP] board today have made a conscious decision to continue to fund activities which not only expose our company to grave reputational risk, but also undermine its economic interest."
The WCA said BHP was wrong to leave because their policies weren't so different.
"BHP is one of the world's largest exporters of coal," CEO Benjamin Sporton said.
"We have compared our position on energy and climate policies with those set out in BHP's Industry Association Review, and believe there are no material differences between the two."