Engen has been proved by documentary evidence in the 11th century for the first time, where it belonged to the Baron of Höwen (also Hewen). In the city area of Engen, there has been a medieval castle, the Burg Neuhausen, remaining unlocated however. In the 13th century, Engen received the city charter.
From 1639, the city belonged to the Count of Fürstenberg, and thus to the Principality of Fürstenberg. In 1640, the area has been devastaded by Swedes and French in the context of the Thirty Years' War.
During the War of the Second Coalition, on May 3, 1800, a battle between the Austrians, led by Paul Kray, and the French, commanded by Jean Victor Marie Moreau, took place, resulting in a retreat of the Austrian troops.
In 1806, Engen went to Grand Duchy of Baden. The city became a district authority in 1846, which however, has been centralized to the district authority of Konstanz during the period of Nazi Germany in 1936.
As a consequence of the statewide local government restructuring reforms in Baden-Württemberg during the early 1970s, the following hitherto independent municipalities have been incorporated into Engen: