With the end of the Roman Empire era and the collapse of the Limes around 260 AD, Alemanni advanced into the land between the Lech and Iller rivers.

Since the second half of the 7th century, the Herrenhof of a Germanic man named Gerfred stood on the site, from which a Carolingian manor farm and later Widdum emerged.

The first mention occurred in 969 in a document by Bishop Ulrich of Augsburg, who transferred goods and income enjoyed by the newly founded monastery of St. Stephen from Abbess Elensinda as a church benefice to Gerfredeshoua.

In 1150, a donation of a Hube with appurtenances in Gereshouen was mentioned in a document of the later Heilig-Kreuz monastery, which was confirmed by Bishop Walther along with other possessions.

In 1904, Gersthofen received the Gersthofen-Gablingen airfield, which was used by American troops as a barracks after World War II and has since been located on the fields of the Gablingen municipality.

After World War II, the population of Gersthofen increased sharply due to the allocation of displaced persons.