Gabbard advised Trump of her intention to step down during an Oval Office meeting on Friday, Fox News Digital reported earlier.
The resignation is effective June 30, it said.
In her resignation letter posted on X, Gabbard told Trump she was "deeply grateful for the trust you placed in me and for the opportunity to lead the Office of the Director of National Intelligence for the last year and a half."
She cited her husband's recent diagnosis with a rare form of bone cancer.
"I cannot in good conscience ask him to face this fight alone while I continue in this demanding and time-consuming post," she said.
A source familiar with the matter told Reuters Gabbard had been forced out by the White House.
In a post on his Truth Social platform, Trump said the principal deputy director of national intelligence Aaron Lukas would serve as acting director of national intelligence.
He said Gabbard had done "an incredible job" but with her husband diagnosed with bone cancer, "she, rightfully, wants to be with him, bringing him back to good health as they currently fight a tough battle together".
Trump has hinted in the past at differences with Gabbard on their approach to Iran, saying in March that she was "softer" than him on curbing Iran's nuclear ambitions.
Gabbard, a veteran and former Democratic congresswoman from Hawaii, built her political name on her opposition to foreign wars.
This put her in an awkward position when the United States joined Israel in launching attacks on Iran on February 28.
During a congressional hearing in March, her measured comments were notable for their careful non-endorsement of the decision to strike Iran.
She dodged questions about whether the White House had been warned of potential fallout from the conflict, including Iran's effective closure of the Strait of Hormuz.
She repeatedly said it was Trump's decision to strike, not hers.
"It is not the intelligence community's responsibility to determine what is and is not an imminent threat," she said.
Gabbard ran for president in 2020 on a progressive platform and her opposition to US involvement in foreign military conflicts.
Citing her military experience, she argued that wars in the Middle East had destabilised the region, made the United States less safe and cost thousands of lives.
Gabbard later dropped out of the race and endorsed the ultimate winner Joe Biden.
Two years later she left the Democratic party to become an independent, saying her old party was dominated by an "elitist cabal of warmongers" and "woke" ideologues.
She later endorsed Trump, who also was a strong critic of past US wars in the Middle East and campaigned on a pledge to avoid unnecessary wars
Gabbard, 44, was born in the US territory of American Samoa, raised in Hawaii and spent a year of her childhood in the Philippines.
She was first elected as a 21-year-old to Hawaii's House of Representatives but had to leave after one term when her National Guard unit deployed to Iraq.
As the first Hindu member of the House, Gabbard was sworn into office with her hand on the Bhagavad Gita.
with AP
