He told the House Intelligence Committee that "it felt pretty good".
The 75-year-old top American spy had been expected to step aside, as President-elect Donald Trump prepares to appoint his own officials.
Analysts believe that he is sending a signal to the Trump administration that they must now speed up the transition.
"I submitted my letter of resignation last night which felt pretty good. I've got 64 days left," he told the committee, indicating that he would stay on in the post until President Barack Obama leaves office.
Committee members jokingly asked him to stay for four more years.
Mr Clapper has authority over 17 different agencies including the Central Intelligence Agency (CIA), the Drug Enforcement Agency (DEA), and the (Federal Bureau of Investigation (FBI).
More than 107,000 employees report to him with a combined budget of over $52 billion (£41.8 billion).
In a profile published by Wired magazine only hours before his announcement, he said that he never questioned the morality of his profession.
In his role, he has often been in the position of defending the National Security Agency (NSA), just one of the covert agencies that his office oversees.
Its image was badly damaged after Edward Snowden revealed how they collect information on American citizens.
During a 2013 congressional hearing, Mr Clapper was asked: "Does the NSA collect any type of data at all on millions, or hundreds of millions, of Americans?"
"No, sir," Mr Clapper replied.
"It does not?" the incredulous senator responded.
"Not wittingly," Clapper said. "There are cases where they could inadvertently, perhaps, collect, but not wittingly."
During Mr Clapper's Thursday testimony, he was asked if Mr Trump will open up a rapprochement with Russia's President Vladimir Putin, but answered that he does not predict a "significant change in Russian behaviour".
Mr Clapper has served in the job for six years after previously working for the US Air Force and the Defence Intelligence Agency.
Clinton crushed Trump, but was that enough? Trump (mostly) did the job; Where Clinton damaged Trump; Hillary Clinton got bad advice; Trump kept taking the bait; How Clinton unmasked Trump; A technical win for Trump; Note to Trump: Talking loud a losing strategy; Debate unlikely to have dramatic impact; Trump lost, but so did all of us
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