Germany had 11 citizens among the 3,000 victims of the September 11, 2001, attacks, according to a report by Deutsche Welle. The victims included people from 92 countries, with three of the four suspected hijackers having recently lived in Hamburg. The Islamist terrorists were thought to have been led by Egyptian-born Mohammed Atta, who had come to the northern German city in the early 1990s to study.

Atta became radicalized, particularly at Hamburg's Al-Quds Mosque, which was later closed by German security authorities. He spent the final three years of his life in an apartment shared with two other suspected attackers in the Harburg district. The so-called Hamburg terrorist cell was believed to have included six men, among them Moroccan national Mounir al-Motassadeq. He was charged as an accomplice in the world's first trial related to the September 11, 2001, attacks. In 2003, the Hanseatic Higher Regional Court sentenced him to the maximum 15-year prison term for aiding and abetting thousands of murders and for membership in a terrorist organization.

German-born Murat Kurnaz was held at Guantanamo Bay without trial from 2006 until his release in August 2006. The Kurnaz case raised questions about why German security authorities rejected his possible return in 2002, despite holding a Turkish passport. Frank-Walter Steinmeier, then-Foreign Minister and current German President, testified before an investigative committee in the German Bundestag about the matter. He acknowledged the suffering of Kurnaz in Guantanamo but emphasized the need to ensure national security.

Chancellor Gerhard Schröder expressed 'unconditional solidarity' with the United States after the attacks, vowing to offer any assistance requested. His remarks set the tone for a series of tougher anti-terrorism laws passed by Germany's Bundestag. These included expanded powers for police and intelligence agencies, tighter immigration laws, and data-mining searches to identify sleeper agents. However, the Federal Constitutional Court later ruled that such practices were legally questionable and that parts of the anti-terrorism database were unconstitutional.

The 9/11 attacks also led to Germany's participation in the U.S.-led war in Afghanistan, which lasted 20 years and ended in August 2021 with the Taliban's return to power. Around 3,600 soldiers from the international forces were killed, including 59 members of Germany's Bundeswehr. Three German police officers also died during the conflict.

On the 25th anniversary of the attacks, the United States told the UN Security Council that 'we hunted down' Osama bin Laden, the suspected mastermind of the attacks. U.S. Ambassador Mike Waltz highlighted the coalition's efforts against Al-Qaeda and ISIS. The UNSC adopted a presidential statement reaffirming its 'unequivocal condemnation' of the 9/11 attacks and condemning all acts of terrorism. However, no response from sources provided regarding the Kurnaz case or the Hamburg cell's activities.