Long before Islam arrived, the Qom region sustained a complex civilization. Excavations at nearby sites reveal settlements dating to the fourth millennium BC, and ruins at Khurha, roughly seventy kilometers southwest, preserve what scholars debate as either a Seleucid temple or a Parthian palace used as a station on the ancient highway. The Sasanian era left more tangible marks: administrative buildings, fire temples, and the fortress known as Qala-ye Dokhtar within the city itself. According to the tenth-century Tarikh-e Qum, the city's name may derive from 'Koomeh,' meaning hut, a reference to the reed shelters built by local shepherds and farmers near the ford of the Qom River. When the Arab conquest came in 644 AD, the area's defenders were likely fleeing Sasanian nobles and returning soldiers. The region remained largely untouched for sixty years afterward, administered from Isfahan and slowly absorbing waves of Arab settlers.

The death of Fatima bint Musa in 816 AD was the event that reshaped Qom's identity forever. She had been following her brother, Imam Ali al-Ridha, to Khorasan when she fell ill and died in the city. From 869 onward, her burial site grew into a structure that was expanded and embellished across centuries, surviving Mongol devastation, Timurid massacre, and Afghan invasion. The shrine became an economic engine as much as a spiritual one. Pilgrims brought money, scholars brought prestige, and by the Safavid dynasty in the sixteenth century, Qom had established itself as a theological powerhouse. The modern seminary system traces its revival to 1922, when Shaykh Abdul Karim Haeri Yazdi moved from Arak to Qom, reigniting a tradition that had dimmed for roughly a century. Today more than fifty seminaries and two hundred fifty research institutes operate in the city, hosting an estimated fifty thousand seminarians from eighty countries.

Qom's history reads like a catalog of resilience. In 825, residents rebelled against Abbasid tax demands, and the caliph's forces killed the revolt's leader and tripled the city's tax burden from two million to seven million dirhams. The Mongol generals Jebe and Subutai destroyed the city entirely in 1221, leaving it depopulated for at least two decades. Tamerlane plundered it again in the late fourteenth century, massacring inhabitants. Afghan invasions in the eighteenth century inflicted severe economic damage. Each time, the shrine pulled the city back. Wealthy patrons funded reconstruction of saints' mausoleums even during the Ilkhanid period, when other sources describe Qom as ruined. The sanctuary of Fatima bint Musa served as a refuge for the Ilkhanid vizier Shams al-Din Juvayni in 1284, proof that the city retained significance even in its lowest moments.

In 1964, Ayatollah Ruhollah Khomeini led his opposition to the Pahlavi dynasty from Qom before being forced into exile. The city's network of seminaries and clerical institutions provided both the intellectual framework and the organizational infrastructure for the movement that would topple the Shah in 1979. Since the revolution, the clerical population has surged from around 25,000 to more than 45,000, and the non-clerical population has more than tripled to roughly 700,000. Substantial flows of religious taxes and alms pour into the city, directed to the ten Marja-e taqlid who reside here. Qom's proximity to Tehran, just 156 kilometers by highway, gives the clerical establishment direct access to the levers of state power. Many Grand Ayatollahs maintain offices in both cities.

Twenty miles northeast of Qom, the Fordow uranium enrichment facility sits buried deep inside a mountain. Iranian authorities chose the location partly because of the difficulty of attacking a nuclear installation so close to one of Shia Islam's holiest cities. The facility became a flashpoint in the long confrontation over Iran's nuclear program. In January 2012, the IAEA confirmed that Iran had begun enriching uranium to twenty percent at Fordow. The facility was struck by the Israeli Air Force in June 2025, and later that month by United States military forces. The juxtaposition captures Qom's contemporary reality: a city where ancient devotion and modern geopolitics occupy the same landscape, where pilgrims and policymakers navigate overlapping worlds.