Following the Hungarian conquest of the Carpathian Basin at the turn of the 9th and 10th centuries, Prince Árpád gave Komárom and the Komárom county vicinity to tribal chieftain Ketel. Ketel was the first known ancestor of the famous Koppán (genus) clan. At the beginning of the 12th century, this tribe founded the town's Benedictine Monastery in honor of the Blessed Virgin, mentioned in 1222 by the name of Monostorium de Koppán. The Turks destroyed much of the monastery and its surroundings in 1529, and the area was thus depopulated. Later references refer to it as the Pioneer Monastery (Pusztamonostor). Presently, it is called Koppánymonostor (Koppán's Monastery) in honor of its founding family. Roman ruins (including a stone mile marker and watchtowers) still stand today. 
The town was heavily damaged in the 1763 Komárom earthquake.
Between 1850 and 1871 the Fort Monostor (Monostori Erőd) was built nearby.
In 1918 Komárom was split by the newly created border of Czechoslovakia. In 1920 Hungary was forced to sign the Treaty of Trianon recognizing the new imposed borders including the border with Czecho-Slovakia. The loss of its territory created a sizable Hungarian minority in Slovakia. The Slovak part is today Komárno, Slovakia. In 1938 the entire city was returned to Hungary, its Regent, Admiral Horthy receiving a tumultuous welcome from the citizens as he crossed the old bridge and entered the formerly dismembered part. At the end of World War II the city was again divided between Hungary and Czecho-Slovakia.
After World War II the occupying Soviets built the country's biggest ammunition storage in the Fortress of Monostor. Thousands of wagons of ammunition were forwarded from this strictly guarded area. One of a series of forts, the Monostor is today open to the public as a museum.
Komárom and Komárno are connected by two bridges: The older iron bridge, and a newer lifting bridge. A third bridge is planned, with the vast majority of funding coming from the European Union's Connecting Europe Facility.
The two towns used to be a border crossing between Czecho-Slovakia (today Slovakia) and Hungary, until both countries became part of the Schengen Area, resulting in all immigration and customs checks being lifted on December 12, 2007.