quality:correction, stylistic:tone
Effects in Afghanistan

If Americans are clamouring to bomb Afghanistan back to the Stone Age, they ought to know that this nation does not have so far to go. This is a post-apocalyptic place of felled cities, parched land and downtrodden people.

— Barry Bearak, The New York Times, September 13, 2001

Most of the Afghan population was already going hungry at the time of the September 11 attacks. In the aftermath of the attacks, tens of thousands of people attempted to flee Afghanistan due to the possibility of military retaliation by the United States. Pakistan, already home to many Afghan refugees from previous conflicts, closed its border with Afghanistan on September 17, 2001. Thousands of Afghans also fled to the frontier with Tajikistan, although were denied entry. The Taliban leaders in Afghanistan themselves pleaded against military action, saying "We appeal to the United States not to put Afghanistan into more misery because our people have suffered so much", referring to two decades of conflict and the humanitarian crisis attached to it.

All United Nations expatriates had left Afghanistan after the attacks and no national or international aid workers were at their post. Workers were instead preparing in bordering countries like Pakistan, China and Uzbekistan to prevent a potential "humanitarian catastrophe", amid a critically low food stock for the Afghan population. The World Food Programme stopped importing wheat to Afghanistan on September 12 due to security risks. The Wall Street Journal suggested the creation of a buffer zone in an inevitable war, similarly as in the Bosnian War.

Approximately one month after the attacks, the United States led a broad coalition of international forces to overthrow the Taliban regime from Afghanistan for their harboring of Al-Qaeda. Though Pakistani authorities were initially reluctant to align themselves with the United States against the Taliban, they permitted the coalition access to their military bases, and arrested and handed over to the U.S. over 600 suspected Al-Qaeda members.

In a speech by the Nizari Ismaili Imam at the Nobel Institute in 2005, Aga Khan IV stated that the "9/11 attack on the United States was a direct consequence of the international community ignoring the human tragedy that was Afghanistan at that time".

In 2011, the U.S. and NATO under President Obama initiated a drawdown of troops in Afghanistan finalized in 2016. During the presidencies of Donald Trump and Joe Biden in 2020 and 2021, the United States alongside its NATO allies withdrew all troops from Afghanistan completing the withdrawal of all regular U.S. troops on August 30, 2021, 12 days before the 20th anniversary of the September 11 attacks, The withdrawal marked the end of the 2001–2021 War in Afghanistan. Biden said that after nearly 20 years of war, it was clear that the U.S. military could not transform Afghanistan into a modern democracy.

The second emir of Al-Qaeda, Ayman al-Zawahiri, a close associate of bin Laden, was killed in a U.S. drone strike at his home in Kabul, Afghanistan on July 31, 2022.