It was recorded as Lytel-Stoke or Lulestock in the Domesday book, and rendered at one time as Little Stock or Little-stoke. Its name is said to have meant "the stoc [farm] of Lylla and his people".
The Blue Anchor to Lilstock Coast Site of Special Scientific Interest (SSSI) provides an outstanding series of sections through the Early Jurassic Lower Lias, spanning the Hettangian and Pliensbachian Stages and named the "Lilstock Formation". This sequence and the good Rhaetian succession beneath are repeatedly affected by faulting, making it of interest to geologists and fossil hunters. It also displays coastal geomorphology which demonstrates a particularly well-developed series of intertidal shore platforms varying in width from about 200-600m. The cliff and beach are rich in reptile remains, including complete skeletons. Lilstock also yields ammonites, shells and fish remains. A unique specimen of an ichthyosaur, named Excalibosaurus costini MacGowan, in which the lower jaw is shorter than the upper was found in the Lower Jurassic Sinemurian Stage, Lower Lias beds on the foreshore at Lilstock and is now in the Bristol City Museum and Art Gallery.
The Acland Baronets were the lord of the manor. Around 1820 Sir John Acland built a boat house on the beach with a pier and breakwater to form Lilstock harbour. Coal was brought from Wales for domestic use on the Acland estate, and to fire the large limekiln on the cliff. Pit props were the main export along with lime. By 1848 there were resident coastguards, and by 1855 a customs officer. About 1860 a stone pier was built from the north side of the harbour wall. By 1866 warehouses were standing beneath the cliff beside the southern harbour wall. The limestone carrier the Richard was wrecked at Lilstock in 1881. A plan for a ship canal from Seaton in Devon to terminate at Lilstock was considered by the Board of Admiralty in 1888. The harbour was apparently abandoned and the pier subsequently destroyed after the first world war.
The sea off Lilstock has been used as an air gunnery practice range connected to RNAS Yeovilton. Lilstock Royal Navy Range, served as a practice bombing range for fixed-wing aircraft using inert ordinance until 1995 when it was redesignated as a helicopter gunnery range.
The small Church of St. Andrew, with only two rows of pews, features a 14th century chancel arch. This arch is the only remaining portion of the earlier Church which was demolished in 1881 when the present structure was erected. The Church was declared redundant in 1980, and the Norman font removed to Stogursey Church in 1981. The church was restored around 1993 but only holds one service a year. The most recent baptism in the church was in 1881 and the most recent wedding was in 1834.