In 1237, Archbishop of Rīga, Nicholas of Magdeburg, ordered the construction of Krustpils Castle, the present-day museum quarters. In the mid-16th century, the castle fell to King Stefan Báthory of Poland and became the centre of the manor that surrounded it. In 1585, the King of Poland gave Krustpils Castle to Baron Nicolaus von Korff. The Barons Korff remained masters of Krustpils Castle for more than 300 years.

After World War I, the Latgale Artillery Regiment was quartered on the premises. In Soviet times, the castle and manor buildings were handed over to the USSR army.

Jēkabpils History Museum has been located in Krustpils Castle since 1996, taking over its management and renovation. Current offer includes tours, exhibitions, displays and educational programmes, rental of premises and different kinds of events.