Kalanick wrote to his employees that he'd spoken with Trump yesterday to "let him know that I would not be able to participate on his economic council.
Joining the group was not meant to be an endorsement of the president or his agenda but unfortunately it has been misinterpreted to be exactly that."
His departure came on the eve of the first meeting of the group at the White House, planned for today.
Disney CEO Bob Iger won't attend either; instead he will be at a company board meeting in California, according to a person close to Iger who requested anonymity to discuss the CEO's schedule.
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Led by Stephen Schwarzman, chairman and chief executive of the private equity group Blackstone, the council has about 15 members, including the leaders of Wal-Mart, Tesla, the Cleveland Clinic and Pepsi.
The council is "designed to provide direct input to the president from many of the best and brightest in the business world in a frank, non-bureaucratic, and nonpartisan manner," according to a Blackstone press release in December announcing its formation.
Yet public outcry about Trump specifically his executive order suspending the country's refugee program and halting other aspects of immigration has put some business leaders in an uncomfortable spot.
Kalanick condemned the executive order and has contributed to relief groups, but calls for a boycott had continued. One woman urging boycotts for all companies tied to Trump said only total resignation from the Trump business forum would satisfy her.
"This is not a 'seat at the table' moment. This is a flip-the-table moment," said Shannon Coulter, one of the organizers of the anti-Trump social media campaign "Grab Your Wallet."
Toby Cosgrove, CEO of the Cleveland Clinic, is planning to attend.
"He has an opportunity to talk directly to the president, and that is a good opportunity," said spokeswoman Eileen Sheil.
Sheil said the clinic employs doctors and caretakers from many countries, and was directly affected by the travel ban. She said a Sudanese citizen who is a first-year resident at the Cleveland Clinic is stuck in Sudan and unable to return to work.