The local Schönau monastery (Kloster Schönau) was founded in 1189 by Philipp von Thüngen.
A Conventual Franciscan monastery since 1699, the monks' main job was to take care of the monastery and pilgrimage church.

The town, which likely had grown out of an early fishing village at the confluence of the three rivers, had its first documentary mention in 1243 in an agreement between Prince-Bishop of Würzburg Hermann I of Lobdeburg and Countess Adelheid of Rieneck.
According to the agreement, two thirds of the castle and half of the settlement were subject to the Hochstift (or secular authority) of the Prince-Bishops of Würzburg.
This followed attempts by the Counts of Rieneck to expand their territory to the south.
At that point, Gemünden had already been awarded the status of town by the Rieneck counts.

The castle above the town, the Scherenburg, had been built by the Rienecks to control the shipping on the Main and the eastern terminus of the Birkenhainer Strasse, an important trade route in the Middle Ages.

The first reference to Gemünden as an oppidum (town) was in a document from 1319.
In 1377, Würzburg took control of the whole town but in 1405 the Hochstift Würzburg sold the town to the Counts of Rieneck, reserving a right to buy it back.
In 1466, Rudolf von Scherenberg made use of this and returned the town to Würzburg.
Under Scherenberg's rule, Gemünden experienced a period of prosperity.
The castle was named after him.
Besides fishing, winegrowing also was an important source of income.

During the German Peasants' War and the Thirty Years' War the town was spared from significant damage.
The town hall was built between 1585 and 1596.
The castle became disused and started to fall into ruin in the 18th century.

The Prince-Bishopric of Würzburg was eventually annexed by Bavaria in 1802.
Gemünden became a Bavarian district seat (Kreisstadt); a railway link followed in 1854, Ludwig's Western Railway, nowadays the Main–Spessart railway.
Gemünden became a railway hub.
In 1872 came the opening of the Flieden–Gemünden line, in 1879 the Gemünden–Schweinfurt line and in 1884 the Gemünden – Hammelburg line.

During the time of the National Socialist régime, the Jewish community's synagogue was destroyed on Kristallnacht (9 November 1938) by SA men.
During the Second World War, many Soviet prisoners of war had to perform forced labour in operations that were important to the war effort.

Owing to the town's strategically important location as a railway hub, two thirds of it was destroyed by Allied bombing raids and fighting towards the end of the Second World War.
In the final days of the war, in April 1945, the railway junction was the subject of fierce fighting which lasted for six days.

Post-war, the railway was rebuilt and Gemünden once again became an important junction.
In 1964, Deutsche Bundesbahn employed 1,200 people in Gemünden.

In 1972, the Gemünden am Main district was abolished.
With the amalgamation of nine municipalities with 14 Ortsteile between 1971 and 1978, the municipal territory increased sevenfold.
The local Schönau monastery (Kloster Schönau) was founded in 1189 by Philipp von Thüngen. A Conventual Franciscan monastery since 1699, the monks' main job was to take care of the monastery and pilgrimage church.
The town, which likely had grown out of an early fishing village at the confluence of the three rivers, had its first documentary mention in 1243 in an agreement between Prince-Bishop of Würzburg Hermann I of Lobdeburg and Countess Adelheid of Rieneck. According to the agreement, two thirds of the castle and half of the settlement were subject to the Hochstift (or secular authority) of the Prince-Bishops of Würzburg. This followed attempts by the Counts of Rieneck to expand their territory to the south. At that point, Gemünden had already been awarded the status of town by the Rieneck counts.
The castle above the town, the Scherenburg, had been built by the Rienecks to control the shipping on the Main and the eastern terminus of the Birkenhainer Strasse, an important trade route in the Middle Ages.
The first reference to Gemünden as an oppidum (town) was in a document from 1319. In 1377, Würzburg took control of the whole town but in 1405 the Hochstift Würzburg sold the town to the Counts of Rieneck, reserving a right to buy it back. In 1466, Rudolf von Scherenberg made use of this and returned the town to Würzburg. Under Scherenberg's rule, Gemünden experienced a period of prosperity. The castle was named after him. Besides fishing, winegrowing also was an important source of income.
During the German Peasants' War and the Thirty Years' War the town was spared from significant damage. The town hall was built between 1585 and 1596. The castle became disused and started to fall into ruin in the 18th century.
The Prince-Bishopric of Würzburg was eventually annexed by Bavaria in 1802. Gemünden became a Bavarian district seat (Kreisstadt); a railway link followed in 1854, Ludwig's Western Railway, nowadays the Main–Spessart railway. Gemünden became a railway hub. In 1872 came the opening of the Flieden–Gemünden line, in 1879 the Gemünden–Schweinfurt line and in 1884 the Gemünden – Hammelburg line.
During the time of the National Socialist régime, the Jewish community's synagogue was destroyed on Kristallnacht (9 November 1938) by SA men. During the Second World War, many Soviet prisoners of war had to perform forced labour in operations that were important to the war effort.
Owing to the town's strategically important location as a railway hub, two thirds of it was destroyed by Allied bombing raids and fighting towards the end of the Second World War. In the final days of the war, in April 1945, the railway junction was the subject of fierce fighting which lasted for six days.
Post-war, the railway was rebuilt and Gemünden once again became an important junction. In 1964, Deutsche Bundesbahn employed 1,200 people in Gemünden.
In 1972, the Gemünden am Main district was abolished. With the amalgamation of nine municipalities with 14 Ortsteile between 1971 and 1978, the municipal territory increased sevenfold.
Gemünden am Main