After the fall of the Soviet-backed Democratic Republic of Afghanistan in 1992, Afghanistan was thrown into civil war between competing warlords. The Taliban eventually emerged as a force capable of bringing order to the country. The rise of the Taliban helped the economy by eliminating the payments that warlords demanded from business people; it brought political benefits by reducing factional fighting (although the Taliban fought aggressively against its enemies, its relative hegemony reduced the number of factions) and brought relative stability by imposing a set of norms on a chaotic society. Although the radical ideology of the Taliban would later alienate many, several observers initially considered its emergence as a positive development. Taliban legend has it that in the spring of 1994, upon hearing of the abduction and rape of two girls at a mujahideen checkpoint in the village of Sang Hesar near Kandahar, local mullah Mohammed Omar, a veteran of the Harakat-i Inqilab-i Islami faction of the mujahideen, gathered thirty other taliban into a fighting force, rescued the girls and hanged the commander of the mujahideen. After this incident, Taliban legend goes, the services of these pious religious fighters were in much demand from villagers plagued by unruly mujahideen, and thus the Taliban were born. (Note: This is legend. The Taliban were already making international news in such papers as the Irish Times as early as first quarter 1990. The part about Omar's involvement may be true, but not about it causing the rise of the Taliban movement as a whole.)

Following this incident, Omar fled to the neighboring Balochistan province of Pakistan, from where he emerged in the fall of 1994, reportedly with a well-armed and well-funded militia of 1,500 followers, who would provide protection for a Pakistani trade convoy carrying goods overland to Turkmenistan. However, many reports suggest that the convoy was in fact full of Pakistani fighters posing as Taliban, and that the Taliban had gained considerable arms, military training, and economic aid from the Pakistanis. Some claim that support also came from the U.S., which would have preferred a Pakistan-installed government over the Russian-backed Northern Alliance.

After gaining power in and around Kandahar through a combination of military and diplomatic victories, the Taliban attacked, and eventually defeated, the forces of Ismail Khan in the west of the country, capturing Herat from him on September 5, 1995. That winter, the Taliban laid siege to the capital city Kabul, firing rockets into the city and blockading trade routes. In March, the Taliban's opponents, Afghan President Burhanuddin Rabbani and Gulbuddin Hekmatyar ceased fighting one another and formed a new anti-Taliban alliance. But on September 26, 1996 they quit the city of Kabul and retreated north, allowing the Taliban to capture the seat of government and establish the Islamic Emirate of Afghanistan.

On May 20, 1997, brother Generals Abdul Malik Pehlawan and Mohammed Pehlawan mutinied from under Uzbek warlord Rashid Dostum's command and formed an alliance with the Taliban. Three days later, Dostum abandoned much of his army and fled from his base in Mazar-i-Sharif into Uzbekistan. On May 25, Taliban forces, along with those of the mutinous generals, entered the undefended Mazar-i-Sharif. That same day, Pakistan recognised the Taliban as the government of Afghanistan, followed by recognition from Saudi Arabia the following day. However, on May 27, fierce street battles broke out between the Taliban and Malik's forces. The Taliban, unused to urban warfare, were soundly defeated, with thousands losing their lives either in battle or in mass executions afterward. Nearly fifteen months passed before the Taliban re-captured Mazar-i-Sharif on August 8, 1998.

On August 20, 1998, US President Bill Clinton ordered the United States Navy to fire cruise missiles on four sites in Afghanistan, all near Khost (and one in Sudan), which the U.S. claimed were terrorist training camps. This was known as Operation Infinite Reach. The sites included one run by Osama bin Laden, the leader of Al Qaeda, who allegedly directed the August 7 bombings of U.S. embassies in East Africa. Three other villages, whose legitimacy as targets was strongly disputed by many sources, were also struck.

At its height, the Emirate was diplomatically recognised by Pakistan, by the United Arab Emirates and by Saudi Arabia. It then controlled all of Afghanistan, apart from small regions in the northeast which were held by the Northern Alliance. Most of the rest of the world, and the United Nations continued to recognize Rabbani as Afghanistan's legal Head of State, although it was generally understood that he had no real influence in the country.

The Taliban received logistical and humanitarian support from Saudi Arabia and Pakistan's Inter-Services Intelligence (ISI). An estimated $2 million came each year from Saudi Arabia's major charity, funding two universities and six health clinics and supporting 4,000 orphans. The Saudi King Fahd sent an annual shipment of dates as a gift. The relationship with Iran was considered poor due to the Taliban's strong anti-Shia policy.