Cook has met with Trump before when several technology CEOs, including Microsoft's Satya Nadella and Amazon's Jeff Bezos, traveled to Washington to meet the president. But he has always had an uneasy relationship with Trump.
The Apple CEO told Trump during last year's meeting that technology employees were "nervous" about his administration's approach to immigration, a source told CNBC at the time. Cook has publicly objected to Trump's immigration stance too, particularly around a policy known as DACA. It is a law that protects certain young, otherwise undocumented immigrants from deportation.
Trump rescinded DACA on Sept. 5, 2017, but as of February, DACA was forced by federal court order to re-open cases for renewals. Another federal judge on Wednesday ordered the Trump administration to restart the DACA program.
"The DACA situation is not an immigration issue. It's a moral issue. This is a moral issue," Cook said in a recent interview with MSNBC's Chris Hayes and Recode's Kara Swisher.
But Cook has been a fan of Trump's tax law which is helping the company to repatriate some of its overseas cash. Apple announced a plan earlier this year to contribute $350 billion to the U.S. economy over the next five years, though did not go into specifics. Trump called Cook "a great guy" after the announcement and called him up to thank him.
—CNBC's Eamon Javers and Catherine Clifford contributed to this report.