O'Brien has "mild symptoms and has been self-isolating and working from a secure location off site," the White House said in a statement Monday.
"There is no risk of exposure to the President or the Vice President. The work of the National Security Council continues uninterrupted," the White House said.
O'Brien, 54, is among the highest-ranking members in Trump's orbit reported to have come down with the coronavirus.
But other administration officials have previously been diagnosed with the virus. Vice President Mike Pence's press secretary, Katie Miller, tested positive for Covid-19 in May. That same month, a personal valet for Trump, who among other tasks served meals to the president, also tested positive.
Kimberly Guilfoyle, an official on Trump's reelection campaign and the girlfriend of the president's oldest son, tested positive in July.
On Monday afternoon, Trump told reporters at the White House that he did not know when O'Brien first tested positive, adding, "I haven't seen him lately."
The White House has said Trump is regularly tested, as are all officials who come into close contact with the president and vice president.
O'Brien earlier this month had traveled to Europe to meet with officials from the United Kingdom, France, Germany and Italy. He was photographed on that trip in close proximity with his European counterparts, none of whom appeared to be wearing masks during meetings, photos from the NSC's official Twitter account show.
More than 4.2 million people in the U.S. have tested positive for Covid-19 and at least 146,900 have died, according to data compiled by Johns Hopkins University.
Bloomberg first reported O'Brien's diagnosis, citing people familiar with the matter. CNN and Politico followed with reports of their own.
-- CNBC's Amanda Macias contributed reporting.