The present village of Bagillt was formed from a number of small settlements, originally mainly the settlements of Coleshill Fawr, Bagillt Fawr and Bagillt Fechan. The name Bagillt is probably derived from a description of an early Mercian settlement, "Bacca's lea" or the lea belonging to Bacca's people. Mercian settlements were common in this part of Wales and at the time Bagillt was settled by Mercian Saxons, it was at the very western edge of Mercia; Offa's Dyke starts at the coast in nearby Prestatyn and Watt's Dyke passes through Bagillt. It is likely that a process of naturalisation to a Cymrycized "-illt" led to the current name.

The Dark Age and early Medieval history of Bagillt was dominated by the skirmishes between Saxons and British. The castle at Hen Blas was established by the Saxon invaders and King Cenwulf of Mercia died there in 821. Hen Blas was in Welsh hands by 1157 when Owain Gwynedd was defeated by King Henry II of England, following which it was refortified as a Motte and Bailey and became one of the three "Royal" English castles in the area. It was recaptured and destroyed by Owain Gwynedd in 1166 to be subsequently rebuilt as a Welsh royal palace. Llewelyn the Great built a chapel there in 1208 but the site fell into ruin following the extermination of the Welsh royal line and the annexing of Wales into England.

Little is known of Bagillt until the late seventeenth century when it became important as an early industrial centre with particular importance for the production of Lead. Later Coal production and various industries, including rope making and brewing became prominent as the village rapidly grew in size. Today it could be said that Bagillt faces a post-industrial time in it's history, the coal and lead works have now gone, new smaller industries have appeared on the industrial estate and many people now commute to the nearby towns of Flint and Holywell and beyond to Chester and the nearby English industrial towns and cities.