The withdrawal extends the US troop presence past a May 1 deadline set by the Trump administration in an agreement with the Taliban but only by a matter of months.
Biden had been weighing the decision for months with his advisers and signalled he did not believe US troops should remain in the country long past the deadline.
Officials were expected to explain the decision further later on Tuesday (Wednesday AEST).
US officials say there are about 2500 troops in Afghanistan.
It’s not immediately clear what will happen to several hundred US special operations forces there that often work for the CIA on counter-terrorism missions.
Those troops are not publicly acknowledged and are not part of the formal calculation of 2500 troops in the country.
Decision would end longest war in American history
Mr Biden’s new September 11 deadline to withdraw US troops would mark a symbolic end to the longest war in American history.
It would come exactly 20 years after the September 11, 2001, terrorist attacks sparked the initial US invasion of Afghanistan.
The Afghanistan troop withdrawal is the first major decision of Mr Biden’s presidency regarding US troops abroad, and Biden wrestled with what to do for months leading up to the May 1 deadline set by his predecessor.
Last month, he signalled he was unlikely to meet the May 1 deadline but said at his first press conference as president that he did not envision US troops remaining in Afghanistan by next year.
“We are not staying for a long time. We will leave,” Mr Biden said.
“The question is when we leave.”
He added, “it’s going to be hard to meet the May 1 deadline just in terms of tactical reasons.”
Secretary of State Tony Blinken laid the groundwork for Mr Biden to make an announcement about the withdrawal in a phone call with President Ashraf Ghani on Tuesday, according to two sources familiar with the phone call.
Blinken did not divulge precise details about the withdrawal but explained that Mr Biden would be calling Mr Ghani on Thursday. Mr Blinken left the Afghan president with the understanding that his US counterpart had decided on withdrawing US troops over the course of the next few months.
Biden administration officials have also been sending signals to Afghan officials at the working level that this was the direction they were headed in, one source explained.
The Biden administration is also making a series of phone calls to allies in the region this afternoon to detail their planned strategy, two diplomatic sources told CNN.
Mr Ghani tweeted on Tuesday that he had spoken to Blinken about planned US-backed peace talks between the government of Afghanistan and the Taliban set for this week and the upcoming phone call Biden.
“Today I spoke with Secretary @ABlinken. We discussed the ongoing peace process, the upcoming peace talks in Turkey, and also spoke about the upcoming phone call with President @JoeBiden”, he said.
Decision comes with risks
The decision to set a deadline for withdrawal comes with risks, as senior military commanders have advocated keeping US troops in the country and have argued a premature withdrawal could lead to a collapse of the Afghan government.
Recent attacks against US forces in Afghanistan have also fuelled concerns. CNN reported last week that the Taliban twice targeted one of the most heavily guarded bases in the country in March and that US military personnel working for the CIA were at the installation when it came under fire.
The US wants to keep an intelligence presence in Afghanistan, according to two sources familiar with the matter.
The annual US intelligence community’s assessment released on Tuesday said prospects for a peace deal between the Taliban and the Afghan government “remain low during the next year.”
“The Taliban is likely to make gains on the battlefield, and the Afghan Government will struggle to hold the Taliban at bay if the coalition withdraws support,” the assessment says.
This content first appear on 9news