"That decision has been made. There will be a significant withdrawal," the official told AFP on condition of anonymity.
Currently, the United States has about 14,000 troops in Afghanistan working either with a NATO mission to support Afghan forces or in separate counter-terrorism operations.
Trump made his decision Tuesday, the same time he told the Pentagon he wanted to pull all US forces out of Syria.
Defense Secretary Jim Mattis quit earlier Thursday, saying his views were no longer reconcilable with Trump's.
The president's twin foreign policy decisions on Syria and Afghanistan are nothing less than epic, and could begin to unspool a series of cascading and unpredictable events across the Middle East and in Afghanistan.
Mattis and other top military advisors last year persuaded Trump to commit thousands of new troops to Afghanistan, where the Taliban were slaughtering local forces in the thousands and making major gains.
Trump at the time said his instinct was to get out of Afghanistan.
The Wall Street Journal reported that more than 7,000 troops would be returning from Afghanistan.
The pull out comes as the US pushes for a peace deal with the Taliban.
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