The term of the FBI director is set at 10 years as an affirmation of the bureau's political independence, and some other chiefs, including Robert Mueller, Comey's predecessor, have served presidents of both parties.
But Comey would be in the delicate position of working with a president who lobbed occasional criticisms from the campaign trail against the nation's premier law enforcement agency. Though attention had centered on whether Comey could have co-existed with a Hillary Clinton presidency, given the FBI's investigation into her email practices and his own public statements about the probe, that question applies at least equally to a Trump administration.
As recently as Sunday, Trump complained that Clinton was "protected by a rigged system" after Comey renewed his decision not to recommend charges for her use of a private email server while secretary of state. Trump repeated his assertion that Clinton was "guilty" and that the FBI "knows it," the bureau's own public statement notwithstanding. Earlier, Trump appeared disrespectful of the Justice Department's independent decision-making power when he said he'd ask his attorney general to name a special prosecutor to take another look at Clinton. That stance went hand-in-hand with "lock her up" chants from some supporters.
Trump's past rhetoric on the terrorism threat, including warnings that "radical Islam is coming to our shores," is out of step with Comey's more measured assessments. And his stated desire to have an improved relationship with Russian President Vladimir Putin comes even as federal intelligence officials have publicly accused the Russians of meddling through hacking in the American electoral process.
FBI officials did not respond to a message about Comey's plans, but James McJunkin, a former FBI assistant director, said he doubted Comey was fazed by Trump's campaign trail statements. He said Comey knew when he was appointed in 2013 by President Barack Obama that his 10-year term would carry over at least two presidential administrations that might differ sharply.
"I can't imagine he would think this is anything more than politics as usual," McJunkin said. "I think politicians say whatever they think they can in order to seize the moment, and I think that once Trump settles into office, he'll realize the value of the independence that Comey displayed."
In three years as FBI chief Comey has been notable for speaking his mind, breaking with White House talking points on matters of race and policing and speaking more forcefully than others in the administration about his concerns about encryption.
That independent-minded streak predates his FBI career, famously surfacing in 2004 when, as deputy attorney general in the Bush administration, he had a dramatic standoff with White House officials in the hospital room of then-Attorney General John Ashcroft over the authorization of a government surveillance program.
Though the White House has not always endorsed his positions and Obama last week appeared to frown on Comey's public statements on the Clinton email matter, there have been no overt signs of the personal animus that's sometimes marred the relationships between other presidents and FBI directors.
But one clear point of division in a Trump administration would come if Trump followed through on the appointment of a special prosecutor. Such a decision rests entirely with the attorney general and does not require the cooperation of the FBI or its director.
So despite Comey's decision not to seek charges against Clinton over her email practices, a Trump-appointed attorney general could name an outside prosecutor to reopen the matter. It's not clear what his plans are, and Trump campaign manager Kellyanne Conway told ABC's "Good Morning America" on Wednesday the matter hadn't been discussed.
"Director Comey is a subordinate of the attorney general, and this is not his bailiwick," said Robert Bittman, who served as deputy independent counsel under Ken Starr.
It's clear from his public statements that Comey would bristle at such an appointment. He has said the FBI's investigation was thorough and that "no reasonable prosecutor" would have brought a case.
Such conflicts over major cases, including the 1993 Waco siege and now the Clinton email matter, are "not new to us," said Robert Anderson, a retired FBI executive assistant director.
Comey understood when he took the FBI job "that it wasn't going to be smooth sailing at every minute," McJunkin said.
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