The site's story begins in 1172 when Hugh de Lacy granted the barony of Skreen to Adam de Feipo, though the manor likely came into the possession of the Cussack family soon after, who built a ringwork castle here as their seat of power. The estate's fortunes changed dramatically in 1401 when Sir Christopher Plunket of Rathregan married Joan Cussack, the heiress to both Killeen and Dunsany. This union brought Killeen into the Plunket family, where it would remain for over five hundred years. Their eldest son John inherited Killeen and his descendants became the Earls of Fingal, whilst the second son Christopher received Dunsany and founded that baronial line.

At the heart of today's structure stands a fifteenth-century rectangular tower house with projecting towers at its northwest and northeast corners. The Civil Survey of 1654 recorded that Sir Christopher Plunket, Earl of Fingal, owned over half the parish including the townlands of Killeen, Clowanstown and Smithstown, with the estate featuring a castle, church, water mill and various outbuildings and cottages. The Down Survey maps of 1656-8 clearly depict the castle as a tower house, which would later undergo significant transformations; remodelling in 1780, alterations around 1804 to Francis Johnston's design, and further embellishments in 1841 by James Shiel that gave the castle its current neo-gothic appearance.

The castle's more recent history has been turbulent; an arson attack in 1981 left it a shell, but restoration works in 2005 saw it repointed and re-roofed. During these renovations, workers discovered two carved stone heads in high relief, one male and one female, on the western façade. Archaeological testing in 1996 revealed part of the tower house's base-batter walls, though no evidence emerged of the earlier ringwork castle that stands about thirty metres to the northwest. These layers of construction and reconstruction tell the story of a site that has been continuously significant to Irish nobility for nearly a millennium.