Michael McKinley, a career diplomat, has served as Pompeo's policy adviser since May 2018 following previous posts as ambassador to Brazil, Afghanistan, Columbia and Peru.
His departure comes as Pompeo and the department have become ensnared in controversy over the Trump administration's dealings with Ukraine that has prompted an impeachment inquiry into US President Donald Trump.
House Democrats have issued a subpoena to Pompeo for documents as part of their probe, which centers on a July 25 call Trump made to Ukrainian President Volodymyr Zelenskiy in which he pressed for an investigation into former US Vice President Joe Biden, a leading Democrat seeking the party's nomination in the 2020 presidential election.
Lawmakers have said Pompeo is not cooperating with the subpoena.
While McKinley has not been directly involved with Ukraine, he has served as a conduit between Pompeo's office and career staff, according to the Washington Post, which first reported his resignation Thursday night.
The State Department earlier this week blocked testimony by the US ambassador to the European Union, Gordon Sondland, who was then subpoenaed to appear October 16.
Former U.S. ambassador to Ukraine, Marie Yovanovitch, is scheduled to appear before the three House committees leading the impeachment inquiry on Friday morning.
McKinley could not be immediately reached for comment on the report and declined to comment to the Washington Post.
The State Department also could not be immediately reached.