Bolton, a retired diplomat who was briefly US envoy to the UN in the George Bush administration, was the third NSA Trump has fired - after former Army generals Michael Flynn and H.R. Macmaster.
"I informed John Bolton last night that his services are no longer needed at the White House," Trump said in a series of tweets.
"I disagreed strongly with many of his suggestions, as did others in the Administration, and therefore I asked John for his resignation, which was given to me this morning.
"I thank John very much for his service," he said, adding that a replacement for Bolton, seen as a hawk especially on Iran, will be announced next week. Bolton had replaced McMaster last year.
The tweet came just one hour after the White House press office said Bolton was scheduled to appear at a Tuesday press briefing along with Secretary of State Mike Pompeo and Treasury Secretary Steve Mnuchin, reports said.
Minutes after Trump's tweet, Bolton tweeted: "I offered to resign last night and President Trump said, 'Let's talk about it tomorrow.'"
The development came amid reports of a sharp rift in the Trump administration over the Afghan peace talks and the proposal to invite Taliban leaders to Camp David, with Bolton staunchly opposing the moves.
Bolton was also unpopular in the administration as he was seen as operating on his own, the BBC quoted White House sources as saying.
( With inputs from IANS )