The castle as it appears today, with its three wings facing north, west and south, largely dates from 19th-century rebuilding, but it follows the footprint of the Inner Ward of a 13th-century masonry fortress built by William Marshal, Earl of Pembroke and Lord of Leinster. Between 1207 and 1213, Marshal transformed Kilkenny into the de facto political capital of Leinster whilst in exile from King John's court; the castle became so grand that in 1210 it hosted the king himself and his enormous army at the start of a campaign to reassert royal authority over the Irish barons.

The original masonry castle, which replaced an earlier earth-and-timber fortification, was described in a 1307 document as having 'a hall, four towers, a chapel, a moat, and other divers houses necessary to the castle'. Archaeological investigations have revealed fascinating details about this medieval stronghold, including surviving circular towers at the northwest, southwest and southeast corners, complete with defensive arrow loops and round-headed embrasures. The substantial stone-lined moat that protected the castle has been excavated on the south and west sides, revealing depths of up to 6.5 metres below current ground level, whilst the north side likely relied on the steep natural escarpment down to the river for defence. The missing eastern wing, demolished in the late 18th century, once contained the castle's main gate-building.

After William Marshal's death in 1219, the castle passed through his sons' hands before eventually reaching the de Clare family in 1247, then the le Despencers, and finally in 1391 to the Butler family, Earls of Ormond, who would own it for nearly 600 years until selling it to the Irish state in 1967. Throughout these centuries of ownership, the castle evolved from a military fortress into a grand residence, though its medieval bones remain visible in the curtain walls, towers and archaeological remains that tell the story of one of Ireland's most significant castles. Today, as a National Historic Property under the care of the Office of Public Works, visitors can explore both the Victorian grandeur and medieval foundations of this remarkable structure that has watched over Kilkenny for more than 800 years.