Kelheim is the site of a large Iron Age oppidum from the La Tène period, which has been tentatively identified with the Celtic city of Alcimoennis mentioned by Ptolemy in his Geography. The ramparts of the fort cross the promontory between the rivers Altmühl and Danube. There is an inner defensive line enclosing 60 ha near the confluence, then a long outer rampart enclosing an enormous area of 630 ha. A small promontory fort on the other bank of the Danube has a series of short linear ramparts protecting a settlement in the bend of a meander. This is aligned with the end of the outer rampart on the far bank, dominating traffic on the river. Kelheim has given its name to the pfostenschlitzmauer style of rampart construction characterized by vertical wooden posts set into the stone facing.
Kelheim was first mentioned in the 9th century. At this time it was the seat of a count (Graf). According to a tradition of Braunau in Rohr Abbey Kelheim has got borough rights in 1151.
G. Schneider & Sohn has a large weissbier brewery in the city.