Stilton was listed in the Domesday Book of 1086 in the Hundred of Normancross in Huntingdonshire; the name of the settlement was written as Stichiltone and Sticilitone in the Domesday Book. In 1086 there were three manors at Stilton; the annual rent paid to the lords of the manors in 1066 had been £4 and the rent was the same in 1086.

The Domesday Book does not explicitly detail the population of a place, but it records that there were ten households at Stilton. There is no consensus about the average size of a household at that time; estimates range from 3.5 to 5.0 persons. Using these figures then an estimate of the population of Stilton in 1086 is that it was within the range of 35–50 people.

The Domesday Book uses a number of units of measure for areas of land that are now unfamiliar, such as hides and ploughlands. In different parts of the country, these were terms for the area of land that a team of eight oxen could plough in a single season and are equivalent to 120 acres (49 hectares); this was the amount of land that was considered to be sufficient to support a single family. By 1086, the hide had become a unit of tax assessment rather than an actual land area; a hide was the amount of land that could be assessed as £1 for tax purposes. The survey records that there were 6.37 ploughlands at Stilton in 1086 and that there was the capacity for a further 1.62 ploughlands. In addition to the arable land, there was 32 acres (13 hectares) of meadows and 10 acres (4 hectares) of woodland at Stilton.

The tax assessment in the Domesday Book was known as geld or danegeld and was a type of land-tax based on the hide or ploughland. It was originally a way of collecting a tribute to pay off the Danes when they attacked England, and was only levied when necessary. Following the Norman Conquest, the geld was used to raise money for the king and to pay for continental wars; by 1130, the geld was being collected annually. Having determined the value of a manor's land and other assets, a tax of so many shillings and pence per pound of value would be levied on the land holder. While this was typically two shillings in the pound the amount did vary; for example, in 1084 it was as high as six shillings (30 per cent) in the pound. For the manors at Stilton the total tax assessed was five geld.

In 1086 there was no church at Stilton.

Coaching Inns

The Roman Ermine Street, which later became the Great North Road, was integral to the development of the village. By late medieval times the village was a popular posting station and coaching stop. At one time there were 14 public houses for a population of around 500.

The main inns of the period were the Bell Inn and the Angel Inn, both of which are still in existence. The Bell Inn has been recorded since 1515 and was rebuilt in 1642. The Angel Inn, dating from the early 17th century, was rebuilt as an impressive red brick house in the 18th century. It ceased to be an inn and was badly burned in 1923. Fires also damaged the village as a whole in 1729, 1798 and 1895.

Modern times

Stilton's reliance on its position on the Great North Road has twice led to problems when use of the road was reduced; the arrival of the railway several miles to the east in the 19th century cut goods transportation along the road, and the opening of a 1.25-mile-long A1 bypass on 21 July 1958 by David Renton, Baron Renton reduced passing trade through the village to almost nil. The bypass was the first from London to Newcastle when the A1 was completely improved in the late 1950s and early 1960s.