"(I) submitted my letter of resignation last night, which felt pretty good," he said before the panel of lawmakers, in response to the top Democrat on the panel joking he hoped he would stick around for another four years.
"I have 64 days left and I'd have a pretty hard time with my wife going past that," Clapper told California Rep. Adam Schiff, who also paid his respects to Clapper's service as the hearing opened.
All members of an outgoing administration must submit a resignation at some point.
Clapper's announcement wasn't a surprise to those around him and was expected at the end of his term. For months, the intelligence director has been updating those around him on his own personal countdown clock, telling them exactly how many days he has left until retirement.
"He signed his letter as required by all appointed administration officials but is finishing out his term," said a spokesperson from the Office of Director National Intelligence. The Office of the Director of National Intelligence announced via Twitter that the resignation will be effective at noon on January 20, 2017.
US faces most challenges now
Clapper's announcement comes as president-elect Donald Trump's transition team is trying to hammer out the people who will lead and set the tone for national security agencies during his administration.
Sen.Mark Warner, the Virginia Democrat and incoming vice chairman of the Senate Select Committee on Intelligence, said Clapper's announcement "underscores the need for the new administration to move expeditiously in making key national security appointments."
"As that process continues," Warner said in a statement, "I hope President-Elect Trump will seek out personnel that embody the same experience, gravity of purpose and service to country that have been a hallmark of James Clapper's career."
While Clapper's job is focused on policy and security, politics intruded at Thursday's hearing when he was asked whether he had any concerns about FBI director James Comey's announcement late in the presidential election campaign that his agency was reopening an investigation into Democratic candidate Hillary Clinton's use of email while at the State Department.
Texas Democratic Rep. Joaquin Castro described Comey's act as an "unprecedented intrusion by a director within our own intelligence community in our democratic process," and asked Clapper if "you believe that Director Comey breached any protocol."
"I have no reason to question Director Comey," Clapper said. "I think extremely highly of him so whatever actions he took he did so what he felt was best and I have no basis for questioning him."
Clapper has said that in over 50 years of military and intelligence work, he has never seen the breadth of challenges facing the US as he does today.
"Our nation is facing the most diverse array of threats that I've seen," he told the committee Thursday.
At the hearing, Clapper was asked which threats will be of most concern to the US in the next 5-10 years.
"I'm hesitant to pick one," he said. Clapper listed the challenges posed by nation states like Russia, China, North Korea and Iran, as well as transnational threats like terrorism, the proliferation of weapons of mass destruction, "which is personally a growing concern for me," he said, and "the challenges posed in the cyber dimension."
Clapper also said that preventing attacks like the June attack on the Pulse nightclub in Orlando, Florida, was among the issues that concern him.
"I will leave this job concerned about the impact of so-called lone wolves and home grown violent extremism," Clapper said. "That is a very complex problem."
Clapper's early career
As Director of National Intelligence, Clapper acts as the principal intelligence advisor to President Barack Obama. He oversees 17 intelligence agencies that range from high-profile places like the CIA, NSA and FBI to groups that were less well-known, like the National Reconnaissance Office.
The office was created in part to end stove-piping within the intelligence community and improve information sharing.
Clapper began his career of 50-plus years in the military, serving as a rifleman in the Marine Corps. He served two combat tours during the Vietnam War, flying 73 combat support missions over Laos and Cambodia. He went on to serve as Director of Intelligence for the war-fighting commands of US Forces Korea, Pacific Command, and Strategic Air Command.
He wrapped up his first government career as director of the Defense Intelligence Agency before retiring and working in the private sector. He returned to government September 2001 to be the first civilian director of the National Imagery and Mapping Agency. He was sworn in as the fourth director of the ODNI in August 2010.