Iran "posed no imminent threat to our nation, and it is clear that we started this war due to pressure from Israel and its powerful American lobby," Kent said in a post on X.
Kent was confirmed to his post last July on a 52-44 vote.
As head of the National Counterterrorism Center, Kent was in charge of an agency tasked with analysing and detecting terrorist threats.
Before entering Trump's administration, Kent ran two unsuccessful campaigns for Congress in Washington state.
He also served in the military, seeing 11 deployments as a Green Beret followed by work at the CIA.
Kent has long been known for his "America First" beliefs and has said he opposes US military interventions abroad.
Still, the announcement came as a surprise, one US official said.
Kent's letter to Trump included "false claims," White House spokeswoman Karoline Leavitt said in a statement.
"As President Trump has clearly and explicitly stated, he had strong and compelling evidence that Iran was going to attack the United States first," Leavitt said.
"This evidence was compiled from many sources and factors."
Kent is close with Director of National Intelligence Tulsi Gabbard, who has kept a low profile since the Iran war began.
Gabbard has not issued any public statements and has only appeared in public during the dignified transfer of US soldiers killed earlier this month during the conflict with Iran.
A spokesperson for Gabbard did not immediately respond to questions about Kent's resignation.
with AP
