The first castle was built as a hunting lodge for King Casimir the Great in the mid-14th century, and it survived in its original form until the 16th. The first modernisation began under King Sigismund the Old (after 1506). A four-wing building with one line of rooms on the eastern and western sides, and two - on the south and north dates back to that time. Inside, the entire building was given a wooden gallery. The northern wing of the castle was designed for residential purposes, and the southern one was used for official functions. At that time, the castle was one of the shelters used by the royal court during the bout of epidemics in Kraków in 1527.

After the damage from the fire of 1550, King Sigismund Augustus continued the work of his father. In 1551-1568, the reconstruction was designed and later supervised by Tomasz Grzymała who enrolled Polish and Italian craftsmen to cooperate in the work. The architecture of the royal castle is based on a design theory by Francesco di Giorgio Martini (d. 1502). The three-storey-high wings with spacious staircases in the corners and the originally wooden galleries built in the second half of the 16th century follow a regular arrangement. The wooden gallery was replaced by a stone one in the 17th century, and early in the 19th century the building was reduced in height by the removal of the upper floor.

Thanks to the influence of Queen Bona, the castle was given a garden of modern design. It was her initiative to establish an Italian garden directly by the southern wing.

Today the castle houses, among other facilities, the Museum of Niepołomice.