The date is beyond the original May 1 deadline that had been negotiated with the Taliban by the Trump administration.
President Biden has been hinting for weeks that he was going to let the deadline lapse, and as the days went by it became clear that an orderly withdrawal of the remaining 2,500 troops would be difficult and was unlikely.
US officials provided details on Mr Biden’s decision, speaking ahead of the announcement.
The news was first reported by The Washington Post.
His decision risks retaliation by the Taliban on US and Afghan forces, possibly escalating the 20-year war.
The move will also reignite political division over America’s involvement in what many have called the endless war.
Setting the September 11 date, however, underscores the reason that American troops were in Afghanistan to begin with – to prevent extremist groups from establishing a foothold in the country again that could be used to launch attacks against the US.
In a February 2020 agreement with the administration of then president Donald Trump, the Taliban agreed to halt attacks and hold peace talks with the Afghan government, in exchange for a US commitment to a complete withdrawal by May 2021.
Over the past year, US military commanders and defence officials have said that attacks on US troops have largely paused - but they say the Taliban have increased attacks on the Afghans.
Commanders have argued that the Taliban have failed to meet the conditions of the peace agreement by continuing attacks on the Afghans and failing to totally cut ties with al Qaida and other extremist groups.
When Mr Biden entered the White House in January, he was keenly aware of the looming deadline and had time to meet it if he had chosen to do so.
He launched a review of the February 2020 agreement shortly after taking office, and has been consulting at length with his defence and military advisers as well as allies.
In recent weeks, it became increasingly clear that he was leaning towards defying the deadline.
“It’s going to be hard to meet the May 1 deadline,” Mr Biden said in late March.
“Just in terms of tactical reasons, it’s hard to get those troops out.”
Tellingly, he added: “And if we leave, we’re going to do so in a safe and orderly way.”