Horningsham enters written history with the Domesday Book in 1086, though the village was certainly inhabited and already called Horningsham in Saxon times. There is also archaeological evidence of Bronze Age and Roman settlements nearby.

In the Domesday Book the village is recorded under two owners, perhaps representing two hamlets, each described as having one 'carucate' of cultivated land (roughly 120 acres, as much as a team of eight oxen could plough in one season) as well as meadows and woodland. One of them had a mill. They were valued at a combined fifteen shillings, making this one of the poorest villages in the area; nearby Maiden Bradley was valued at £10.

By the early 1100s the village had been bought by a French Norman family, the Vernons, who had fought at Hastings.  For their main residence they built Woodhouse Castle, to the west of Horningsham, possibly during the reign of King Stephen. The castle survived 500 years but was destroyed during the Civil War. 

The Vernons built the Church of St John the Baptist in 1154. The tower which stands  today is said to date from the 1400s though the rest of the building was rebuilt and enlarged in the mid 1800s. 

A later John Vernon, Sheriff of Wiltshire, endowed an Augustinian monastery at Longleat in the 1200s. By the early 1500s this had become a Carthusian Friary. It was sold off at the time of the dissolution of the monasteries and ended up in the possession of John Thynne, who bought it in 1540 at the age of 25 for £23. John had not been born wealthy but amassed huge riches as the Steward to the Duke of Somerset, brother of Henry VIII's third wife Jane Seymour. John built Longleat House (or started it; additions were being made up until the early 1800s) and his descendents still live there today. The title Marquess of Bath was given to the family by George III in 1789.

A number of Scottish builders came to the village during the construction of Longleat House, and lived in an area that is to this day called 'Scotland', behind the village pub. As religious non-conformists, they lacked a place to worship and met at first in the woods, until John Thynne gave them a patch of land to build a meeting house. There is doubt that the Chapel on Chapel Street is the original building, but it is thought to be the oldest Methodist chapel in continuous use in England.

During the 18th century the village prospered through weaving, a cottage industry. After the invention of the spinning jenny, a mob of 500 marched from Corsley Heath to pull down a gig installed in a mill owned by a Mr Everett. It seems that this event in 1767 somehow came to the attention of Karl Marx a century later when he was writing Das Kapital;  he mentioned it with huge exaggeration as a riot involving 100,000 people.

The Thynne family now own most of the village, though that was not always the case.  The first area they bought after buying Longleat was Little Horningsham, to the south of the main village, which came with a manor house that the family allowed to decay. They did not own the entire village until the 1700s.

The village has shrunk greatly over the past 150 years. From a peak of 1,800 in 1836 the population has fallen to around 350, and a number of cottages have disappeared. Little Horningsham no longer exists, apart from one cottage by itself at the very end of Pottle Street.

Whereas there were once four pubs, there is now only one. 100 years ago there were a doctor and a policeman living in the village. They have both gone, as have the village forge and, most recently, the village shop. However the village still has a thriving primary school, a busy pub, an active Village Hall, a Cricket Club, monthly services in the Methodist Chapel, and a full calendar of village social events throughout the year, including a popular traditional Village Fayre every June.